So he has a bunch of broken links in the various Libraries? In other words, he tried to merge them on disk himself, and the source files are now all mixed together and all the links are broken? Ugh. I almost mentioned up above to make sure not to try to move the files around on disk until you were all, completely, totally done (then just Rename, Move, Copy them to whatever final destination you want).
Wow. Nightmare hellride. If a bunch of the Libraries have a portion of files that aren't broken links in MC, you can still use method #2 above to preserve metadata on whatever is left and not broken. Then, just auto-import what is left at the end.
So:
0. Seriously, make Library Backups of each Library first and save them somewhere safe.
1. DO NOT MOVE ANY MORE FILES ON DISK UNTIL YOU ARE DONE.
2. Pick whichever Library is in the best shape to begin with and use a clone of that as your new Master Library.
3. Maybe, try to fix as many of the broken links as are possible in the Master Library with Rename, Move, and Copy files in "update database only" mode.
4. Then open up one of the to-be-deleted Libraries and get ready to make your MPLs.
5. Before you start, make
an IsMissing Smartlist, select all, and remove them from the Library (assuming they can't be easily fixed by doing Rename, Move, and Copy in "update only mode").
6. Do the MPL exporting/importing steps I outlined above.
7. Repeat for all other to-be-deleted Libraries.
8. Return to the Master Library, and run a final import to grab the rest. When you do this import, set a
Tag On Import rule to auto-tag all of the new files with some [Keyword] or something you can search for later (to "separate" them from the stuff you saved via the monkey-steps above).
9. Make a final Smartlist to show just those files with the keyword you made when you imported them.
10. Finally, use the Fill Properties from Filename tool to save as much metadata as you can get from the file/folder structures on disk.