Plex Media Server removes from index Movies updated externally

Plex Media Server is working fine for me on Ubuntu 15.10, except for this odd behaviour:

I have Dune:
Movies/Dune (1984)/Dune (1984) 720p.mkv

I deleted this file previously, and then restored it a few days later.

Plex will no longer re-index the file, or seemingly anything in this folder.

I have a similar problem with Ghostbusters, the file of which I replaced (without deleting). It doesn't appear in the Movies index no matter what I do.

1. Where can I find scan logs to track this down?
2. Any idea what's causing this?