Serial uploads always go to memory slot 0 of your Oak - no matter what is in that slot. A factory Oak boots to 0 looking for the system firmware, so if you upload via serial, you essentially wipe the ability for your Oak to do natively do OTA updates and firmware updates. If you want to restore that ability, you'll need to use follow the instruction on how to restore your Oak to factory defaults.

I'll come back and document the Serial update process within the next day or so, if I get it working…