Collections/Playlist management

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For the first issue, if you have networked storage (e.g., a NAS), you may want to disable the scheduled task that cleans up playlists on start. That may be where your items are going. If that's not the issue, please either recreate the issue or grab logs from where it has happened and upload them to privatebin.net while removing any sensitive info.

Can I use these collections in another library with a custom title, without moving the media from its original folder?

This doesn't make sense to me. Collections draw from existing libraries. You could go into the Metadata Manager and change the name "Collections" to "Bananas" but it will still draw from your existing library of media.

Some of my collections aren’t keeping the correct title. Whenever I try to change them, they revert to the old title after a scan—or I’m not sure why. Additionally, I’ve seen movies appearing in collections where they don’t belong. Removing them doesn’t work, as they get re-added after a scan. I’ve tried enabling the "Block changes" option, but that didn’t help.

Check the metadata on the incorrect movies. They may have been misidentified previously and now have a TMDB box set ID which pulls them back in. Deleting this excess metadata should resolve the issue. If not, rinse and repeat what I said above: logs may help to identify what's going on.