I recently updated MC's library on one of my rarely-used machines to match my others (simply copied the library data folder from the shared location over to the "new" place on the other machine). The "new" machine (which isn't really new, but we'll call it that for simplicity) doesn't access the files in the same locations as the others (or even the same set of files), but I do like it to have to same View Schemes and everything. So, when I update the library on it, I usually copy the library data files over, open MC, select all the media and delete it (remove it from the library). Then I simply re-import the new files. I've done this a bunch of times in the past, and never had any problems. This time, I noticed two weird things though...
1) This is small, but when I deleted all the media out of the library (after I fixed problem #2), and then ran the Import Media tool... When it did the "Analyzing Library" step it still Analyzed all the 28,000 files I had just deleted (and which all weren't accessible from this machine). I actually did close out of MC and re-open it before I ran the import too, so it was weird... Made the import process take much longer than was needed. I couldn't get these "phantom" files to go away until I checked both the "Fix or Remove Broken Links" and "Include network and disconnected drive types" boxes. It showed that it was removing all the files which I had already removed manually...
2) After I went to my "All Media" view scheme (which is simply an empty top level view scheme created using Marko's instructions from when we lost the old top level scheme), selected all, deleted (choosing option 1 in the delete dialog)... MC still contained a bunch of media files, which were listed under the Playlists group, but which didn't show up anywhere else! I think I figured out where these came from, but it's a bug for sure...
Back prior to 11.1, I had a "Step 4" search entered into the Top Level "Library" View Scheme (which prevented any sub-view schemes from listing certain files which I usually didn't want to see). This included CDA files and files which I added the genre "hidden" (usually weird thumbnails, system sounds and videos, and similar stuff). So that I was still able to access these hidden files through MC, I had (under the old "Advanced" view scheme) a couple of child schemes that had the "Honor Parent Scheme Search Strings" deselected -- so they'd show everything.
Fast Forward to Today. I'm using 11.1.186 and doing my above-explained operation. As I said, I noticed that even though I went to All Media (which is set up to show everything in my library -- Step 4 is blank) and deleted everything, MC still has a bunch of files listed under "Playlists". Turns out that all of these are the "hidden" files!!
Even though there is no longer a top-level "Library" view scheme, it is apparently still applying the searches I had entered into the old one from the pre-11.1 library!! If I turn off "Honor Parent Search Strings" in my All Media view scheme (which was empty and is itself a top-level view scheme now), then all those hidden files appear. This is really no good, because there's no way to access the searches to edit them or delete them. Thankfully mine are fairly benign (imagine if I had a search to exclude all Images or something equally silly in there), but still...
I was able to test this by changing the Genre on some of my new existing files (after finishing the re-import) to "hidden". They (poof) disappeared. If I dug them back out (by unchecking Honor Parent Search Strings and changing the genre back to what it should be), then they would come back. There's no way for me to get rid of this search, because it's being applied to a view scheme that no longer exists (or at least that is hidden so I can't get to it).