In trying to understand your issue let me see if I have this straight.
You have a part file and a derived mirrored part file that are fine prior to checking into the vault.
You check them in and somewhere in the checkin the derived looses its connection to the original part.
While in the vault you see nothing as far as geometry in the viewer or are you saying that if you check it out again the mirrored portion is lost.
What does your feature tree look like before checkin? Do you see the external reference symbology?
My guess is that if this is the case, you can check on the external references dialog and see a path
that is being lost in the checkin.
Is there a link between the two part files? If you try checking out the mirrored part, does the dialog also list the parent part? If you do a where used on all versions of the parent part, does it list the mirrored part?
I have had this issue on at least 3 parts but every time I manage to find that a very same geometry error in the original part is causing the problem. Once the error is fixed the geometry in the mirrored part comes back...
Try rolling back in the feature tree of the original model to a point where there is just basic geometry and see if the geometry shows up again. If it does then you have to hunt down the issue and fix it.
Normally for me the issue has been geomtery that is bad but the problem doesn't show up until I round the part and make the geometry even worse.