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Unless things have changed drastically since I last used Pro/E with TCe (which is possible), then re-naming was also a real pain in the butt.
At that time it was limited to a command line operation and had to be done on each item individually and in the correct order. If you made one mistake it was back to the drawing board - and that was with a TCe guy on-site actually modifying the code as we tried......
The interrupted upload issue proved to be a big problem also due to the corruption issue you have already mentioned.
End conclusion - no 3rd party system will handle a CAD apps data as well as the system from the same manuafcurer. Windchill deos a great job of handling Pro/E as you would expect but even then there are certain things that are still far from perfect. If PTC can't get it right every time, then 3rd party suppliers are always going to have an issue.
We see similar things with Windchill when handling CATIA, UG & Solidworks data. It works reasonably well, but nowhere nearas smoothly as with Pro/E data.
Simon Lucas