11 days ago - AndrewT - Direct link
RMS Oceanic said: I see the Launcher says the Mod is no longer on the disk
We've certainly had reports of this message, although I thought that was about mods that had been removed from the Steam Workshop.

Brutal but perhaps you could flag those files read-only?  
10 days ago - AndrewT - Direct link
I'm not aware that the launcher deliberately edits mod files - that would seem pretty strange to me! But I don't use or have anything to do with mods so I can't say 100%.

If you upload this mod to the Steam workshop or our mod site, then subscribe to it, do you get similar problems?