Nextcloud is an application managing both files in a storage and file records in a database… other records exists only in the DB a(as you point out calendar and contacts)… if you want “restore” which by definition reverts an application to specific point in time then you need to restore both parts and loose changes performed in between…
In your situation having old backup, and new records existing in undamaged DB, restoring only the files might be a good alternative to full restore. running occ files:scan --all and occ files:cleanup should fix issues with the files… given the assumption a file version is a file with special-crafted filename I would expect versions state is good as well (reverted to the state of backup). AFAIK metadata lives in DB so it should survive… Disclaimer: I didn’t test this - just my “educated guess” so you might want to perform a backup your existing state and use it in case restore efforts still brake something…
I would never go this path… there is no supported way to restore only subset of the database and you remain in danger something brakes (long term) and in the future you will never know if some issue results from the tampered database…
regarding the cron - take a look at “examples” provided with official Docker image… we had lot of discussion regarding cron with Docker here in the forum as well…