G'Day eljr.
I guess it can be pretty intimidating deleting bits of MC and trusting it will rebuild itself. Just so you know, I did do this to one of my local (on local hard disk) libraries before posting. It has just 1056 files in it, but it rebuilt all thumbnails within two minutes, just by me scrolling around MC. It was too quick for me even to need to run the "Build Missing Thumbnails..." function! Basically, as soon as I looked at a view, the thumbnails were built. I will note that the rebuilding wasn't reported in the Reporter using that method, but I believe it would be for larger libraries when the "Build Missing Thumbnails..." function is run.
My experience is that it is a reliable and repeatable process.
Never mind, you have your Cover Art now.
You may be interested to know that when you insert a CD into an optical drive with MC running it looks up metadata in the JRiver online database, YADB, using the Album version of that database, which is pretty good and often finds CDs. (There is also a YADB Track database which isn't so good at finding individual tracks.) If it doesn't find it in the YADB database it looks up freedb online. This metadata (Artist, Album, Track names, etc.) is saved in a CD database within the MC Library and is shown to you before you rip the CD. That is what enables you to edit the metadata before running the rip processes. Even if you don't actually rip the CD, that metadata is stored in MC. When you delete the Album from MC, that metadata
and any modifications you made to it are still stored in MC.
Also, when you delete an Album from MC that has been ripped or imported, all its metadata is stored in a "Removed" database in the MC Library.
So when you re-rip or re-import that deleted Album, MC has four databases it can retrieve metadata from; the two Online databases, the CD database, and the Removed database. (If you re-import just tracks it only uses the YADB Track database.) I believe that the original metadata already stored in the MC is used instead of looking up the online databases, and I think the Removed database gets precedence over the CD database. I haven't exhaustively tested that, but it is consistent with my observations and what others have said.
You can set up Views to look at what is in the CD and Removed databases, and you can edit records in there to correct them, or delete records if they are wrong and you want MC to refresh its data from the online databases. I have been able to add Cover Art to the CD database for CDs that I have never ripped! Neat.
So, this CD that unexpectedly got its Cover Art back without any intervention from you probably had Cover Art already stored in your Cover Art directory, and the metadata MC already had about the CD probably pointed to that Cover Art, which was likely stored in the directory defined on "Options > File Location > Cover Art > Folder". Or MC could just have looked up the Cover Art on the Last.fm site or elsewhere using the metadata it already had.
That final CD that has no Cover Art, and for which the art disappears when you try to update it? That old art would just be a thumbnail in the thumbnails database, with no corresponding Cover Art file. That is why it disappears. You effectively break the link to the thumbnail by trying to replace the Cover Art associated with the CD. If you have tried to add any new Cover Art and it hasn't taken, you could look in the Cover Art directory for it, and if it is there, a right-click and "Cover Art > Quick Find In File / Cover Art Directory" may find it. I think this is a symptom of the thumbnail database indexing being slightly corrupted, which my procedure was intended to fix.
With "boxed sets" I'm no expert as I haven't had to do it yet. At least not with CDs. It isn't supported in a standard way in MC, so there are a few different approaches I have seen threads discussing. If you find some threads about it, and see how people approached it, then work out how you want to do it, I'm sure MC can be made to accommodate your requirements. The main issue is to work out what you want MC to do.
Thanks for the positive feedback. Understanding how Cover Art works has been one of my "things" in MC.