I've been ripping a few BD in the last nine months. Only five actually, now that I look. They all still have their "index.jpg" files and Cover Art shows correctly. I also get the Cover Art using "Get Movie & TV Info...".
I doubt that MC is deleting the files, but I wouldn't be surprised if something else is. Very possibly a security application. I can never make much sense of the MC logs, so can't really comment on what you have provided, other than to say there is nothing really obvious. I would understand if the thumbnail build overwrote the index.jpg file, but not just deleting it.
The best idea I can think of is that most web pages used to have the default file set as index.html, and also some used an image, named index.jpg. With all the scams, malware, Trojans and so on, some security software tried to prevent fake web servers being created on your system, to act as part of a BOT network or such. So they deleted any landing page/file, index.html, that they found, and probably also took out index.jpg. That could be what is happening I your case.
Or maybe your Linux MC Client has some web server components installed, or security software, and is scanning the disk and removing the index.jpg file, as part of a lost web server?
Is there any pattern to the ones that get deleted, like they are the movies you have watched?
If you really want to know what is deleting the file, and the network drive is running on a Windows Vista or later system, you may want to turn on Auditing for the directory or index.jpg files as per this thread:
https://social.technet.microsoft.com/Forums/windowsserver/en-US/971e24e2-462e-41a8-a8ba-e39140508dc7/how-can-track-who-deleted-filefolder-from-windows-server-2008?forum=winserverfilesOr maybe even run the trial of
FileAudit mentioned in that thread to see if it captures anything. I don't know what the trial restrictions are though, and it isn't something you would want to buy for home use!