My Solution on the same situation
Create a checks_tmp/ directory on a different storage volume that has sufficient available space.
Set Proxmox Backup Server (PBS) into maintenance mode (offline).
Move some chunk directories from the original location to the checks_tmp/ directory.
Create symbolic links pointing from the original location to the new temporary location.
Example:
# mkdir /checks_tmp/
# cd /mnt/datastore/pool2/.chunks/
# mv /mnt/datastore/pool2/.chunks/ffff /checks_tmp/
# ln -s /checks_tmp/ffff /mnt/datastore/pool2/.chunks/ffff
Run garbage collection.
After the garbage collection has finished, remove the symbolic links and move the directories back to their original location.