We have had the same issue... here is what I understands happens.
EPDM and SolidWorks both keep track of file references.
When SolidWorks opens a file and it needs to load an external reference it follows the standard rules for finding references - See help.
EPDM keeps track of the external references of all files and 'attempts' to update the references in the SolidWorks files when they are cached to the local disk. Normally that works just fine but sometimes not.
I have not been able to trace exactly why EPDM cannot update the references of certain files. We only had an issue with files that were migrated to EPDM and then renamed / moved but not with all files. The most common issue we have is a Drawings.
Are this issue solved? We are having the same problem...
references in SOLIDWORKS are managed in several areas and are stored/changed when checking in a file. You can use the Tools > Update References functionality when importing files into PDM to make sure all references are updated correctly.
You can also add the external location in the Administration Tool under Local Settings > Settings > External References. I would be careful though and add a warning when checking in files with external references (user/group settings > Warnings > Check In > Outside SOLIDWORKS PDM).
From my personal experience, I can tell that situations can be different, and there is no universal decision probably.
There are cases when something can be solved by means of the references updating, or the SolidWorks or PDM settings.
But, there are cases when it does not help. Everything depends on the problem reason.
I do not guarantee the accuracy of statements, but in simple words it can be described so: SolidWorks saves internal identification in the file on purpose not to allow accidental changeover of the file by other file (in some situations such warning appears).
I do not know why, but it is interesting that by means of EDrawings - files open without problems (in case of this SolidWors, PDM, Treehouse, etc. cannot open these files). Information on references still somewhere means is?
So far, I found the only way to solve similar problems (but only in a case when in the file there is information on external references).
It is simple to check existence of information on references - to select the necessary file from SolidWorks and without opening it to press the button - External References.
If references is, but specify in other location - with high probability it is possible to try everything to recover - having moved folders / folders with files to the specified directory.
After that it is possible to open and copy / move assembly.
It is also possible to try to change External References.
But if there is no information on references in the file just (for example because of any error),
at the moment, I have no other decision except manually to specify a way to each file to SolidWorks.
Perhaps there are more reasonable decisions, but I think them it is necessary to try out of PDM.
I and now have many such files without references (because of failure of the server).
Such files cannot be moved to PDM normally.