Use the link below to view an article from 2001 that explains in some detail relevant information to some of your issues. Keep in mind that is written from an earlier revision of Pro/E but the methods and concepts are still relevant and take note of the hyperlinks in the page regarding the reference viewer and it's functionality.
From your description it may be renaming of some models without the parent object(s) being in session that is causing your issue but using the steps outlined in my article you should be able to re-establish the lost references and recover your work. I had a Pro/Toolkit developer working for me at the time but did not think it worthwhile to try and automate this. We could usually resolve the lost references quickly and it does require some "thought" to get it done that may be tricky to implement in Toolkit.
http://https//web.archive.org/web/20020110010852/http://profilesmagazine.com/p16/tips_copygeom.htmlhttps://web.archive.org/web/20020110010852/http://profilesmagazine.com/p16/tips_copygeom.html#
If the link does not work let me know and I will see if I can dig up the doc.
