This is a longer known, annoying bug in this plugin:
https://tracker.moodle.org/browse/MDL-69570
I can't understand why it isn't still not fixed.
In our moodle we have to clean up these orphaned files (10GB every week) continuously with moosh and bash-shellscripts.
I don't have moosh installed, so my approach is different, although still using bash. It assumes that you have a separate DB Server to connect through ssh, but that can be changed easily. The select statement creates a deletelist shellscript which is then executed and removes the physical files. Afterwards the db entries in mdl_files are removed.
mytime="1 YEAR"
sqluser"yourusername"
sqlPW="yourpassword"
#create deletelist script
ssh user@yourserver "mysql -u$sqluser -p$sqlPW yourmoodle_db -e \"SELECT DISTINCT CONCAT('rm -f /path/to/moodledata/filedir/', LEFT(mdl_files.contenthash, 2),'/', MID(mdl_files.contenthash, 3, 2),'/', mdl_files.contenthash,';') AS shellscript FROM mdl_files WHERE component = 'assignfeedback_editpdf' AND timecreated < UNIX_TIMESTAMP(DATE_SUB(NOW(),INTERVAL $mytime));\"" > clear.sh;
#modify and execute deletelist script
sed -i '1d' clear.sh
chmod +x clear.sh
/path/to/clear.sh;
#delete database entries
ssh user@yourserver "mysql -u$sqluser -p$sqlPW yourmoodle_db -e \"DELETE FROM mdl_files WHERE component = 'assignfeedback_editpdf' AND timecreated < UNIX_TIMESTAMP(DATE_SUB(NOW(),INTERVAL $mytime));\"";
