Watching this anxiously.
I'm not an expert on the APs, I don't even own one (yet) but I do work in the computer industry and see corruption happen a lot.
The one thing I'm confused about in this case is where the data is stored. Does the AP "flash" the ECU and then just monitor it after or does the data "live" on the AP itself and the ECU references it? If the corruption happened on the AP I would try to find some way to do a factory reset or contact Cobb they may be able to get you a copy of the devices OS files. Even if you reload the maps there could be something wrong with the operating system on the device causing the problem after maps are reloaded. If the data "lives" on the ECU and has become corrupted the remarry and reload will probably work. Is there any possibility of physical damage to the AP? Even just excessive heat from sun exposure or intense vibrations can wreak havoc on electronics.
You say: "Cobb AP V3 had a message about the data being corrupt an needing to be restored. I clicked OK and proceeded with life."
Did it give any other information? Did it say what would happen when you clicked ok? Any kind of error number or code? I would hope that the AP would create a backup of the factory map before flashing. I would also think that if the data on the AP were corrupted it would attempt to flash the ECU back to the backup it made of the original configuration. That would explain why you were running so lean, etc.
The first thing we need to figure out is what data got corrupted. Device OS, Device Maps, or data on the vehicle's ECU. The answer to that will determine the fix.