JSONDB will only have backups of Things and Items and the like defined in PaperUI. Your bindings and whatever has gone wrong to break PaperUI for you will not be there.
That being said, if you were to start over, grabbing JSONDB and the conf folders should preserve much of your configuration to migrate to a fresh install.
Just things got broken (lost). Thing file in jsondb was empty. Dont know why. Found some 172kb thing files in backup folder under JSONDB, stopped service, restored the last one of those, restarted service. Everything is working again.
I did not know why things where empty after the reboot. Filesystem seems not to be damaged.
The missing file would be an indication of the sorts of things that can happen when a Pi loses power. If OH was writing to that file at the time of the power loss the entire file can disappear.