Did you ever get a solution to this? Considering doing the same thing you are with PTC data and I'm fearful of unsupported formats within EPDM. Are you still getting crashes?
So far the best compromised configuration is to install the Renamer Add-in on the server and not the pro/e connector on the clients. This way when a creo file is saved in the vault it will removed the .x numbers at the end of the file. The only drawback is there are no configs shown on the data cards of the creo files, which may be good enough.
We have a smattering of about 7,000+ creo prt, asm, & drw files. Lots of family table prt and asm. I tried to bring them all into the vault over a couple weeks but when doing some data validation I noticed that some of the family table instances were not showing up as configs on the data cards. Those missing config tabs on the data cards seemed to coincide when I had to kill the xtop.exe process to unfreeze Windows Explorer - Not Responding error. These particular creo files would also then be corrupted and cause creo to crash when trying to read them from the EPDM vault. I would get a Traceback error log from Creo.
Another observation is that it was best to bring items into the vault in the order of PRT first round, ASM next then DRW. I have not had a chance to use the XML import tool to see if it works better.