[drwyrm]

@drwyrm That refresh in between was a test, and I think the result means that Kodi does something a bit differently when scanning in a TV show this way vs the other. Do series stay split like they are supposed to when they are added with a library update when "exclude this path from collection update" is disabled, then Artwork Beef after? I assumed this was yes but I better make sure. I'll try to recreate this.

No, with "exclude this path from collection update" disabled, it still merges series. I started checking this option to avoid the bug after it made a mess on a full library scan because my downloader triggers automatic scans after a finished download.

The problem really is related to the .NFO files, they were exported by an ancient version of Kodi at least 3 years ago. I removed all .nfo files and rescanned(same full scan that made a mess earlier) the directory tree and the problem no longer happened. I have a backup of the .nfo files here that I made in case you want to try to reproduce it.
Here is the backup of all the nfos I renamed to avoid the bug, directory structure preserved: https://mega.nz/#!5oBgSQQT!cpImi_3WMQ27r...bWfSmXMSWg