Rather than beat your head agains the wall I would do a new backup now via PSE, I name my backups "Full 12272012" so I know when I did them. If I have an incremental(I don't do incremental normally) I name it "Incr 12272012". After you do this delete all your other backups. You may want to do it twice for safety, naming one -1 and the other -2.. After that you can begin the next phase of sorting out the pictures. I also use an EHD for my backups and keep my catalog and pictures on a different EHD.
That's appears to be a sensible suggestion & I'll try to create new backup's.
What I think will be a much bigger problem still remains that of all the duplicates & possible some that might be triplicated & I have no idea as how to tackle this.
This leaves all of my other questions in the original thread unanswered.
If you write your tags to file(I think in 11 it has changed to metadata, it is under file) all your tags will be placed within each photo, this way you don't lose your organization. At this point you have a few solutions, all a lot of work.
You can have PSE look for duplicates and start churning through the results. I haven't been impressed by this approach, not very robust.
If you find an outside pgm just have it churn through your pictures. I have never used these but if there is a good one I would like to know.
Since you have written your tags to file you can reload all your pictures into a new catalog. I think you will lose your Albums, stacks and version sets, but that may be a small price to pay to get yourself out of the duplicate problem. This approach gives you the most control and I feel is not as overwhelming if you just do a folder at a time.
Good luck in this project.
I would suggest you do a backup frrequently, minimally once a week.
Maybe someone will come up with a better solution.
I suspect that one drawback to using 3rd party programs to look for duplicates is that it appears that PSE 10 doesn't keep the pictures real name but assigns it an arbitrary number as a shortcut that points to it, or at least this is the impression I get from looking into a catalog. Whats why I asked just what all the files that are assigned by the program & what they actually do would be helpful.
I don't know much about the interals of the catalog so I can't hep you there. My understanding was that the catalog had a pointer to your actual picture, did not do any renaming. If you are looking at the backups that is Elements own convention, nothing to do with your actual pictures, I would just not worry about the backups and its conventions. If you use a 3rd party to delete the duplicates(or whatever, move them to a new location) they will show up in the catalog as unconnected, then you can delete all the unconnected from the catalog.