IT Tips & Tricks

How to Prevent Missing Data in Data Migration

A practical guide for IT teams

Published 14 November 2022

Updated 18 May 2026

A while back, a group of us showed up at a coworker’s house to help rebuild his porch. Although it should have merely taken us one productive morning, it ended up taking a full day.

Brian had all the materials neatly organized. The plan was solid. Everyone knew what they’d be doing. But as we got started, something became obvious pretty quickly: There were missing pieces.

A few more boards were required. We needed more L-brackets. Some measurements didn’t 100% line up. Without these things, a couple of important connection points simply wouldn’t, well, connect, and we had gaps. Suddenly, what should have been a straightforward build turned into a fair bit of backtracking, problem-solving and rework.

That’s exactly what happens in IT when data goes missing during or after a data migration or a file system reorganization project. Sadly, many teams don’t even realize they have missing data … until it’s too late.

Many teams don’t even realize they have missing data … until it’s too late.

It shows up during a migration, an audit, or when a user says, “This file should be here, but it’s not.” Or, “There’s a bunch of stuff missing from dozens of these Excel spreadsheets!” And at that point, you’re not just managing systems. You’re reconstructing what should have happened.

If you’ve ever managed a data migration, large-scale transfer or system consolidation, you’ve probably experienced this firsthand: Just because the job finished doesn’t mean the data made it intact.

This guide is for IT managers, migration teams and consultants who want to avoid that scenario altogether by understanding where missing data often comes from and how to prevent it before it becomes a major problem.

Why Missing Data Happens More Often Than You Think

Going back to Brian’s porch, the good news is that nothing failed outright. We didn’t get an error message saying, “Porch build unsuccessful.” But we had gaps and we had to figure out why. And that’s what makes missing data so tricky in IT environments. It’s rarely caused by one obvious failure. Instead, it’s usually the result of small issues that compound over time. Here are some of the most common root causes:

1. Changes to File Locations Without Updating References

When file locations change, whether through folder restructuring, renaming or other reorganization, any links pointing to those files usually break. The file still exists, but the new location means the link no longer works.

2. Lack of Visibility Into File Relationships

Most systems don’t track how files are connected (such as spreadsheets linking to other files, embedded paths in documents). Without this visibility, it’s easy to move data without preserving link relationships. This has been the source of all manner of other problems.

3. Incomplete or Interrupted Processes

Transfers and migrations can appear successful although:

Task runs may encounter files that fail to migrate to the destination, without generating visible error messages.

Task runs may skip items when source or destination permissions prevent access.

Task runs may complete only partially when network interruptions occur, leaving some data sets unmigrated.

4. Permissions and Access Issues

Data may be in storage but become inaccessible if permissions fail to transfer correctly. In these cases, users may experience the data as “missing,” even though it technically exists.

5. Reliance on Process Completion Instead of Data Validation

Many teams assume that when a task run completes, the data is accurate. But without validating what actually arrived, gaps go unnoticed. Post‑migration validation should include checks for file counts, folder structures, permissions, metadata integrity, and link resolution to confirm that the destination truly matches the source.

These issues are dangerous because they often remain undetected. Task runs may complete without surfacing errors, leaving missing files, broken links or incorrect permissions hidden until users encounter them later. The absence of visible failure signals creates a false sense of success, masking gaps that can compromise operations.

The Hidden Risk: “Successful” Migrations That Aren’t Complete

Imagine finishing the porch, stepping back and realizing, with a rapidly evaporating air of satisfaction, that the railing is skewed or the screen door is missing because someone forgot to frame it in. Sure, the job is technically “done.” Functionally, however, it’s a problem.

Not a bad day’s work for a bunch of IT guys, right?

In IT, this shows up as:

Missing or inaccessible files.
Broken references between documents.
Incomplete datasets that only surface later.

This is especially risky in:

Migrations from file shares to modern platforms such as SharePoint, Egnyte or Box, for example.
Managed File Transfer (MFT) environments.
Compliance-driven industries.
Large-scale storage reorganizations.
Cloud migrations.

Even a small gap can create outsized consequences, such as:

Audit failures.
Compliance exposure.
Lost productivity.
Erosion of trust in the system.

How to Prevent Missing Data (What Actually Works)

1. Don’t Just “Build It” — Validate What Actually Moved

With Brian’s porch, we didn’t just assume everything was there. We had to stop and double-check what was actually there. Same with migrations. Don’t rely on process completion alone. Validate:

File counts (source vs. destination). For example:
- A 2 GB PST (Personal Storage Table) file could become a 1.6 GB file due to truncation.
- Zero-byte placeholder files get created when transfers fail.
- Duplicate files inflate counts but hide missing originals.
File sizes and integrity. Instead of just checking size, for example, compare:
- Checksums or hashes between source and destination.
- File headers for known formats (PDF, Office docs and so forth).
- Last modified timestamps (watch for unexpected resets).

This catches silent corruption that logs won’t display.

Completeness of transferred data should always be validated. Watch for partial files that did not fully migrate and stub files that appear as placeholders in cloud or tiered storage environments. Confirm that files which were complete in the source remain complete in the destination and verify accessibility rather than relying only on metadata presence.
Files may migrate as stubs (metadata without full content).
Stub files may trigger delayed retrieval or fail to open when accessed.

These often pass migration checks but fail real-world use:

Permissions. A file that exists but can’t be accessed is effectively missing. Check, for example:
- ACL (Access Control List) mismatches.
- Broken inheritance.
- Lost group mappings (especially with Active Directory changes).

Validation means testing real-world usability, not just the presence of the data. This is where most migrations quietly fail. Ask:

Can users open linked Excel models without errors?
Do embedded document paths still work?
Do applications that depend on file paths still function?

If not, sure, your data is “there,” but it’s unusable.

2. Keep the Connections Intact

One of the biggest issues with Brian’s porch wasn’t just missing boards and brackets. It was the corner connections that didn’t line up and the almost-missing screen door.

In IT, those “connections” are file links and they’re far more fragile than many teams realize. When files move, links break in very specific (and often overlooked) ways, such as:

Excel external references that still point to old UNC paths after migration.
Word and PDF embedded links pointing to file shares that no longer exist.
Links embedded in Access databases and legacy apps that fail when hard-coded file paths no longer resolve.
Reporting tool connections that break when static file locations change.
Shortcut files and mapped drives that silently fail when drive letters or server names change.
Relative vs. absolute path mismatches, where moving one folder breaks entire chains of dependent files.

The result? The file is technically there, but from a user’s perspective, it’s gone.

The result? The file is technically there, but from a user’s perspective, it’s gone.

That’s what makes this problem such a pain. It’s not always missing data. Sometimes, it’s disconnected data. And at scale, manually finding and fixing these broken relationships is nearly impossible.

This is where LinkFixer Advanced™ comes in: automatically protecting file links before a migration (so those connections stay intact even as the underlying data moves) or repairing broken links afterwards.

3. Find the Gaps Before They Become Problems

We didn’t wait until the porch was finished to notice something was wrong. We caught it early on, sent Brian to the hardware store and quickly got back on track. Tim “The Toolman” Taylor would have approved.

Your migration process should work the same way, but most don’t.

Instead of waiting for users to report missing files, you should be actively looking for the “gaps” before and during the process.

Run pre- and post-migration comparisons, such as:
- File counts and total storage size.
- Folder structure mismatches.
- Missing or newly created directories.
Identify orphaned files, for example:
- Files that exist but are no longer referenced by anything.
- Files that were referenced but didn’t make it over.
Track skipped and failed files by error type, such as:
- Path length limitations (>260 characters).
- Locked or in-use files.
- Permission-denied errors.
Detect zero-byte or partially transferred files:
- These are common in interrupted jobs or unstable network conditions such as dropped TCP sessions, packet loss, high latency or SMB (Server Message Block) timeouts. In these cases, files may only partially transfer or fail mid‑stream, leaving incomplete data at the destination.

Discover “hidden failures,” such as:
- A job that may be flagged as successful even though warnings, skipped items or incomplete transfers are buried in logs. Files can look present but be partial or stubbed. Permissions may silently fail to carry over and embedded links can break without triggering alerts.

The truth is that once users start saying, “That file used to be here,” you’re no longer ahead of the game, you’re behind (and getting bombarded with complaints).

4. Build Validation into Every Phase

A good build doesn’t wait until the end to check stability. A good migration doesn’t either. Teams that avoid big problems treat validation as a continuous process, not a one-off final checklist.

a) Pre-migration: Understand what you actually have

Crawl the system to map:

File locations.
Inter-file dependencies.
Link relationships.

Identify:

Long file paths.
Unsupported file types.
Deeply nested folder structures.

b) During migration: Monitor what’s actually happening

Track:

Files skipped due to errors.
Throughput anomalies (sudden drops may indicate issues).
Retry attempts and failures.
Log why files fail to transfer, not just that they failed.

c) Post-migration: Validate usability, not just presence

Recalculate and compare:

Checksums for data integrity.

Test:

Opening files from user environments.
Linked documents and dependent workflows.
Permissions and access rights across groups and roles.
Application integrations (databases, reporting tools, legacy apps).
Shortcuts, mapped drives and UNC paths.
Relative versus absolute path dependencies.

Scan for:

Broken links.
Missing references.
Permission inconsistencies.

Remember that a file that exists but doesn’t work is just as problematic as one that’s missing.

5. Avoid Manual Rework

Trying to “fix it later” is like attempting to frame in the screen door after the porch is already fully assembled and screened in. It’s slower. Harder. And usually involves undoing work you hoped was already finished.

Data migrations are no different. Manual fixes often create more problems than they solve.

They don’t scale. Fixing a handful of broken links is manageable. Fixing 5,000 is not.
They potentially introduce new errors, such as incorrect path updates, missed dependencies or inconsistent file fixes.
They drain time and resources when skilled IT staff are stuck doing repetitive cleanup.

Automation changes the equation with:

When you get it right, you can chill instead of stressing

Bulk link updates instead of one-off fixes.
Repeatable, rule-based corrections.
Full visibility into what changed and why.

This helps keep migrations consistent … and recoverable if something goes wrong.

Where LinkFixer Advanced Fits In

If the goal is to avoid missing data, you need more than just a way to move files. LinkFixer Advanced offers that and more: It’ll help you avoid downtime, lost data, upset end-users and angry bosses.

But those benefits are secondary to its primary purpose, which is to protect linked data. This is how you ensure:

File relationships stay intact.
Links are automatically protected and repaired.
Data integrity is preserved across environments.

That’s exactly what LinkFixer Advanced is designed to do. It can:

Identify and repair broken file links both before and after migration.
Maintain connections during migrations.
Protect data integrity.
Reduce manual effort and risk.

LinkFixer Advanced is fast and efficient and nothing else in the world works quite like it when it comes to handling vast numbers of file links. And when we say vast, we mean it. Hundreds of thousands or even millions of links can be protected, preventing data loss and ensuring a smoother migration.

Make sure every piece of data, and every connection, arrives exactly where it should.

And how fast is fast? In the time it takes a proficient IT guy to locate and repair a single link, LinkFixer Advanced can find and fix about 6,000 of those suckers, making it an essential migration power tool.

This means that when your migration is complete, you’re not left rebuilding pieces after the fact. And user complaints about missing data? Zero, zip, nada.

Final Thought: Build It Right the First Time

By the end of a long day, we finally got Brian’s porch finished, but not without the extra effort and bookoo added time that we could have avoided if everything had been carefully considered up front. That was the real lesson.

In IT, missing data doesn’t always come from big failures. Sometimes, it comes from seemingly small gaps that go unnoticed … until they matter.

You can test drive LinkFixer Advanced with a free trial, chat with us online or call 727-442-1822 to pick a consultant’s brain. If you’re understaffed and migrating to SharePoint, you may want an expert to help guide you or fully handle the migration for you.

At the end of the day, the best teams don’t just move data. They make sure that every piece, and every connection, arrives exactly where it should … just like Brian’s screen door.

Feel free to share this article on your social media: