The only way to preserve the created thumbnails is to close MC and backup the library files and the corresponding thumbnail files outside MC so that they are perfectly synced. You can restore the backed up files outside MC and on the next startup MC will use the files without knowing anything about what possibly happened after the files were backed up.
When you say backup of files outside MC you are thinking of copying library files and cover art without the MC backup tool right? All the .jmd files? I'll try that as soon as I have cleaned up my library. Just to have said it once again; why the heck you can't save the thumbnails with the backup tool is beyond me though.
I got one additional problem now! The 4000 albums added are mostly duplicates of my existing tracks
Most of them was probably not deleted at all. I selected ALL library fields and compared them one and one. Not so supprisingly the Play conter, skip counter etc. are reset upon import. As well as modified import date and so on. Ratings etc are kept. The only thing I can see that is different than those things are the "Compression" field. My old tracks in library have "CBR (MPEG-1 Layer 3)" and the new ones have "CBR (MPEG-1.0 Layer 3)" data in the field. Maby it was the other way around? Is this enough to make the duplicates?
Can anything bad happen if I rename all my "CBR (MPEG-1 Layer 3)" to 1.0 with the search and replace tool? I'll try it on one album. Only problem is that this only represent 2800 of my 4000 tracks. So there is probably something else as well. This is certainly looking more and more like a nightmare.
Update:
I tried to do a Find and Replace, but the Compression field could not be selected. Instead I updated the library from file tags, and sure enough, the Compression fields changed from 1.0 to 1. I then enabled the auto import again, but the files on the album got duplicated again!
This time there are no difference in any fields except from the obvious ones.
Tried to do a normal import of the album as well, but it got duped there too. "Imported 12 new files. Updated 12 files that had external changes" it say. I really don't get this. Help with this one will forever be remembered!