Were the files checked-out before the vault was moved?
If so, that is your problem.
The workspace keeps track of which fileserver where the file came from.
Unfortunately, the client attempts to send the file back to the same fileserver during check-in.
This should be a bug, but PTC never addressed it.
The workaround is to delete the file from the workspace, check-out a feresh copy and continue from there.
Do not simply Update the file. You must delete and check-out fresh.
When you change only the attributes and check-in, only the meta-data is updated in commonspace.
Intralink knows that the file itself has not changed and does not upload it during check-in.
The result is that the new version (commonspace object) uses the same file as the prior version.
This is intentional behavior to minimize disk usage.