is that reddit post also from you? The initial post seems very similar in details and wording.
Either way, I have not been able to find any cases with a customer facing a similar quandary, but I did find a few cases where FortiManager was linked to downstream FortiGates and caused sync issues due to deleting unused objects.
One solution in those cases was to simply disable fabric sync:
config system csf
set fabric-object-unification local
This would stop objects from being synced to AND from the FortiGate in question. To my knowledge, if you disable this on your root FortiGate, it should simply stop further object syncing, but already synced objects should stay in place and be unaffected.
Aside from that, the best solution would be to have all FortiGates added to the FortiManager, so the manager can handle objects across the entire fabric, not the root FortiGate. You could open a ticket with Technical Support to get some assistance in migrating your entire Fabric to the FortiManager, not just the one root FortiGate, but this would certainly take some time.
+++ Divide by Cucumber Error. Please Reinstall Universe and Reboot +++