Alright I spent some time learning bcdboot and bootrec today. :) Something about the "Repair" totally hoses the boot configuration, and I can't explain it, nor fix it. The very strange thing is that during the repair it reboots 2-3 times and does so without issue.

Before I mucked with fixing the above FileHistory issue, I took a backup and I am glad I did. I was able to manage to get that working (there was YET ANOTHER problem with not being able to access the network, despite valid credentials -- so moved it to a local disk which took a bunch of time).

Once back on the pre-"Repair" everything worked again, but I was still facing the same File History issue.

So what I ended up doing was "Repairing", then configuring an empty File History configuration in the "Repaired" mode and then doing a rollback on the "Repair." This yielded a working File History and bootable OS. Win. :P