By Chris Turner
After a large Vault migration, users may occasionally find that their file references need refreshing in order for the correct files to be found by Vault. This is sometimes the case when migrating from older versions such as 2010 or 2012.
Files migrated from previous releases of Vault may have incomplete references. Vault will show the parent or child files in the "Uses" or "Where Used" tab. However, if a file is renamed, moved, or has a copy design action performed on it, issues may start showing. Files may be blocked and not downloaded correctly. In some cases, Inventor files do not pull the ‘children’ or associated linked documents when opening them from inside the Autodesk Inventor application
To resolve this issue, you can update file references in the Vault. It can be done on individual files or whole folders if necessary. Be careful if you choose a large amount of data (like the $ root) as this may take a number of hours to complete depending on the size of your Vault.
You can perform an "Update File Reference" by selecting a file or folder and then going to ACTIONS > UPDATE FILE REFERENCE
A dialog will appear and a progress bar will show as follows. 
When the update is complete, any errors found will be displayed, you may now manually repair these references individually.
The "Update File Reference" is a very useful tool, especially when migrating from very old versions of Vault.