I shouldn't complain as my missing FTM 2012 media is miniscule compared to yours although I have not tried a large merge such as you describe.
I'm was also using Windows 7 (although I have now chg'd to W8) and have abt 1700 media items located within FTM's Media folder. I noticed several weeks ago that many of those files were no longer there. I spent some time re-inserting those files from primary pdf/jpg locations elsewhere on the pc and now recently noticed 2 were again not linked (there may be more as I have yet to check them all).
I don't know that the 2 newly-found missing links are repeats or not but it's a little frustrating that FTM can't seem to maintain those files in the FTM Media folder.
While my 'problem' seems minor (in count) to yours and has other differences, I had to go item by item in the Media section of FTM to manually re-insert those 'lost' media files. Hopefully someone else will reply with a more timely fix for your problem.