So short version, I moved Skyrim from my C drive to my D drive. And yes, I did that part properly and Skyrim itself, SKSE, and ENB are all working fine when started through Steam or through their own executables. After doing so I went into MO's executables menu and made all the appropriate changes (starting directory and executable locations).
Now if I start SKSE through MO like I've always done Skyrim doesn't load any data files. And I mean ANY data files. On trying to load a game one of the files it complains is missing is Skyrim.esm. So....yeah. Running SKSE or TESV directly everything works fine (except, of course, that all my mods are in MO so they're missing).
Papryus is logging nothing at all and MO's logs show only normal activity, no errors or warnings.
Any idea how to fix this? Preferable while preserving my mods and profiles, but if I absolutely have to set those up again I can.