Try it from the other direction. Create a new session on your target drive and import tracks and data. It is critical to COPY the source media, not REFERENCE the source media (except for the video files). If Pro Tools encounters duplicate filenames in different directories, which may be what has happened to you, it will resolve the duplicate names by appending a .1, .2, .3, or dot-whatever, so the new session contains all unique filenames. Two or more files may contain the same audio but they will no longer have the same name. The downside to this is that you will not always have whole filenames in your bin list. The upside is that the new session will contain ONLY audio that is actually used, no lingering junk, just as if you had cleaned your region list and Saved Copy To. Error -39 is not a filename problem, though, so I'm not sure you've identified the actual problem. Error-39 usually means there is a corrupted file somewhere, or the timeline is corrupted. Importing tracks one or two at a time can help identify where the problem is, at least isolate it to a specific track. Eventually you'll find the problem.

OF course! I swear, i'm going to end up with a permanent imprint of my own palm on my forehead. I'll try it this way. Thanks, Richard!

breck when that solution doesn't work take all of your audio files, put them into 1 audio files folder, do not replace duplicates...after your done moving files take the left over duplicates, and put them in a folder named something like Zaudio. Now import your session data to a new session copying media, and when it prompts you to relink missing files choose MANUALLY select just your audio files foler and hit relink choose by NAME not unique identifier...this is very important relink as much as you can to your audio files folder when this is finished, relink to your ZAUDIO folder again, by name only now if this doesn't work may i suggest trying in Nuendo...it asks which duplicat you would like to use i love this feature

Sorry to be late with a reply. I was out with the worst flu I've ever had in my life!! Actually, Richard's suggestion worked perfectly. Thanks!!