The other table to truncate mdl_task_adhoc as that is a tracker of the background backup processes.
In code/admin/cli/ there is a backup.php script. Suggest running that script with parameters to save the course backup to a destination outside of moodledata/filedir/ and use a command line 'nohup' wrapper (no hangup).
So that command issued from code/admin/cli/ would look like:
nohup php backup.php --courseid=2 --destination=/moodle/backup/ & [ENTER]
Your command line prompt will come back and you could log out then but ... you might want to stay and watch progress a little bit.
CourseID the id of your large course. You manually create the destination directory. The nohup & wrapper will put the command in a no hang up wrapper and execute until completed. It logs to a file 'nohup.out' at that location and you could watch it's progress via:
tail -f ./nohup.out
Or from command line, in your moodledata/temp/backup/ directory a contenthash named directory will be created to build the backup .mbz file and you could continually ls -l inside that directory to see activity.
In the GUI, in the cateogry of courses where those are located, there should be a listing of those pending and there should be a trashcan. Click the trashcan to remove it from the listing.
While the GUI says one can move onto other things, think it's been discovered that in reality a user may have only one of those running at a time.
All in all, best to use command line for large courses like that. Good luck!
'SoS', Ken