I ran a couple of commands to delete all the disk temperature notifications which brought me from ~14000 notifications to ~4200. Archiving works now.
If anyone runs into this in the future, these are the commands I used:
# delete all notifications that have "temperature" in the filename
rm -v /boot/config/plugins/dynamix/notifications/archive/*temperature*.notify
# delete all notifications that have "returned to normal temperature" in the text content
grep -lr '/boot/config/plugins/dynamix/notifications/archive/' -e 'returned to normal temperature' | while read -r line ; do
rm -v $line
done