A lot going on with a Moodle these days ... autobackups that had already been set and used might be contending with recyebins now.
Check recyclebin settings ... set to show all the time in a course. Also set it to keep whatever for the shortest amount of time. That will hurry along courses/files/etc. to the trash.
You might wanna check into a CLI adhoc_task.php script in code/admin/tool/task/cli/
On another server having issues with what appeared to be 'ghost' backups in moodledata/temp/backup/ turned out to be the deletion of an assignment in a course that all students on the system had to turn in ... a 1 minute video X 600+ students.
Had to run:
nohup php -e adhoc-task.php &
and let it run for hours.
See help for script php adhoc_task.php ... there are other options which one might need to turn on or set.
'SoS', Ken