I'll assume that this is a feature request and not a bug in the artwork handling
If I specifically link album artwork to a file, I'd like MB to remember that "saved" link, even if I do "Rescan All Files" or "Rescan Artwork"
For example, with boxsets, I have the main box artwork in the folder with all the tracks.
With "Enable Image Rotation" on, I want the CD specific artwork to be included but I don't want the artwork from all the other CD's in the box set to display (tracks from CD1 are playing so only boxset and CD1 artwork not artwork from CD2, CD3, etc), so I turn off "include sub-folder" in my Artwork retrieval settings and put my individual CD artwork in sub-folders Disc1, Disc2, Disc3, etc. Save the track specific artwork with the "link to the original picture file" option.
All works fine until I need to do a full rescan, then all the links to sub-folders are lost and I have to manually re-link all that artwork.
Not fun at all!