in such cases, we have to delete module by module, I guess. That worked, but found that for one of our instances, there were still many GB of data in the moodledata filedir, so probably it was data which was not referenced in the database, due to earlier site cloning.
cd /the/moodle/directory
moosh file-dbcheck > /path/to/filestodelete.txt
Then I just edited the filestodelete.txt to pre-pend sudo rm -f to each filename in the list, and ran it to get rid of around 8 GB. Completed in less than a minute.
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