If I re-call correctly, Moodle doesn't immediately delete anything. When one removes a file from the new file system and it's not linked anywhere else in any course, Moodle moves it to the trashdir. The contents of trashdir gets cleaned every 4 days - IF one runs cron. No cron. No emptying of trashdir. So your space usage might have been in the trashdir all along ... or it could also have been in the moodledata/temp/backup/ directory where the backups are built and then copied to whatever you've chosen to save/retain backups.
Since I've not read of anyone doing what you are doing (although it is perhaps a fix that will work) cannot say for sure what the consequences would be. But, there is a readme.txt file in filedir. Please read it.
What you've done is intelligent and I understand the reasoning behind it, but the goal now should be to get it operate as it should ... without the work-arounds, etc. in place.
If there are files in moodledata/temp/backup they can be removed manually without affecting anything. Think the same might be true of anything found in trashdir ... although Moodle might complain about not finding anything there it was told to delete it should not be a critical error that would prevent Moodle from functiong.
Have to remember, that now, with the new file system, one is not only working with physical files (which are an adventure to find) but also a database. It's very important when backing up now to have both an SQL dump of the database AND the datadirectory.
At this point, I don;t think one has to re-install, but one should keep an eye on backups ... any kind of backup now that you know where to look and for what to look.
It would be wise to test one of your course backups in the same production environment ... restore to another hidden course. Or restore to a local version of Moodle running on your laptop/workstation.
And, one more thought, with your provider ... can you acquire some more space (more wiggle room)? Yes, it won't be for free, but think of it kinda like insurance.
My 2 cents, of course.
'spirit of sharing', Ken