Not that I have it all figured out, but it sounds like it would help to decouple backup from sync. I have syncthing keep a two-way sync, including deletes, but have syncthing's trash as a "backup" (items deleted after n-days) on each device in case I accidentally delete something. Then I have a nightly, encrypted backups with versions stored offsite (eg borg) which is only meant to be used if there's major failure like a flood or fire. HDD failure is covered by RAID10 NAS. Somewhere in there I have or need a data integrity/hash check, but at least it's a start.
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