Recovery seems to have worked! Thanks to the instructions from @stephan here
In short,
Kill all processes after checking with “ps -ax | grep cryosparc” as described here
reboot
backup/rsync /software/cryosparc/* to an external just in case
Then Stephan’s commands to restore the database:
eval $(cryosparcm env)
cd cryosparc2_database
mongod --dbpath ./ --repair
cryosparcm start and “Database configuration is OK.”