Edit: Never mind - the issue is due to PMS finding the file by checking the full path, but the folder not showing up during a scan. I don’t know the root of the issue yet, but it’s unrelated to Plex. 
Server Version#: 1.13.9.5456
Running on Ubuntu 16.04
Recently moved all my files from my old NAS to a new one and followed the procedure here, as I have done several times successfully in the past. I have disabled “empty trash after library scan”, because PMS was deleting and re-adding all the library items during the daily mantenance (but not during the other automatic scans or when I manually start a library scan, though). While the items now stay in the library, a bunch of things will show up with a red trash icon over the poster - despite Plex being able to play them. I dug into the logs, and here’s what I see in Plex Media Scannner.log:
Nov 22, 2018 05:37:54.103 [0x7feb19c17800] DEBUG - Looking for path match for [/data/audio/audiobooks/A Song of Ice and Fire (Audio Books 1-5 - Complete)/1 - A Game of Thrones/ASOIAF - Book 1 - A Game of Thrones - 64 - Daenerys VIII.mp3]
Nov 22, 2018 05:37:54.104 [0x7feb19c17800] DEBUG - Path matched, we're reusing media item 2134962
[a bunch more stuff]
Nov 22, 2018 05:49:03.376 [0x7feb19c17800] VERBOSE - Softly removing media item 1759812 part 2358729: /data/audio/audiobooks/A Song of Ice and Fire (Audio Books 1-5 - Complete)/5 - A Dance With Dragons/51 ASOIAF - Book 5 - A Dance with Dragons - 50 - Daenerys VIII.mp3
Nov 22, 2018 05:49:03.376 [0x7feb19c17800] DEBUG - Soft-deleting media item 1759812.
I think the issue might be that Plex has somehow ended up with a different media item # for the same file. Anybody else encounter this issue and has an idea how to fix it, that doesn’t include doing the Plex dance? I have a bunch of friends on the server and I’d like to avoid trashing their watched status.
