I partially found the cause. I looked in the client log and found it was reporting corrupt mods. In each of the affected mod folders the mod_info.lua files had been renamed and the initial part of the file name appended with my computer name (so mod_info-COMPUTERNAME.lua). Why I'm not sure. It's only happened in my mods folder and nowhere else on my system. I back stuff up so restored from a backup and it's fine. No indication that it's a virus either so I'm suspecting an issue with backup software, one drive (which also copies my faf mods folder through a hard link) or the client itself. If anyone else has a clue I'd be interested to know.
