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We recently upgraded to 3.4 M063 (didn't here about that one did you) and WF4.0 M060.
It now appears that many (not all) of our PTC Library files (family tables) are now shown with a ? mark and are no longer locked by the administrative user. When a user checks out an assembly and subsequently saves it all of the family table instances need to be verified.
There are tens of thousands of files in our libraries.
This seems to have happened (or was noticed) by a group that just recently switched to WF4.
BTW M063 fixed the WAN problem I mentioned in my only other post.