Well, all I can say is '350 Gb course' beats my 130+GB course. :|
And yes, 1.9 -> 3's site has probably developed many issues not yet discovered. :\
Question now is ... what to do about it ... on shared business plan we know no tweaks to DB are possible ... but cleaning out moodledata/filedir might be possible but one could also have to clean up meta data in DB. So if you try below, make a DB dump of the DB before attempting ... that's if you can install a thing called 'moosh'.
https://moodle.org/plugins/view.php?id=522
it's a command line only tool but it does have a couple of commands one can run to find 'orphaned' files ... and remove them - physically from sea of files in moodledata/filedir/ + the rows in mdl_files that refer to them.
https://moosh-online.com/commands/
And ... will say this, since you are in this situation with a 'shared' lease, might be time to xfer hosting to a VPS where one does have control over tweaking what needs to be tweaked.
Yeah, that probably means it cost more, but isn't your time (what you really pay yourself) worth something?
My 2 cents!
'SoS', Ken