Sorry for this discussion with myself but maybe that will be useful for others.
What I did that helped so far:
- search for all tracks that have an Cover Art image pointing to a "Media Center XX" folder (instead of being inside)
- created the "Media Center XX/Cover Art/Albums" folders with all the versions I needed
- copied all the cover art images I have in those folders
- ask Media Center to create thumbnails for all those tracks in the search results (Cover Art/Rebuild Thumbnail option) -> it refreshes the cache/database and most of the cover art shows up now
- ask Media Center to move the cover arts to the latest version folder (Cover Art/Save Convert Art to External Location defined in Options) -> It copies the covers to Media Center 29 folder and updates the info in the track tags/database too.
- Some tracks don't get updated because the cover file is missing
- I now have to deal with only the tracks that still have cover art pointing to older versions but search for them again since those tags haven't been changed. There is much less albums now!