No sure if this has been mentioned as this thread is getting quite long. Just a quick heads up. I have flashed my ECU today (2022 R) successfully and upon restart of the bike using the TuneECU procedure, the check engine light did come on. I checked the error via TuneECU and it was the crankshaft adaption error. I never did any resets after the flash as it has been suggested, but this error did show up. I was using TuneECU v5.6.25. A quick crankshaft adaption reset via the tuneECU software any the error is gone.
For those not sure - make sure your bike is running, is up to temp (96c), then via TuneECU menu find the crankshaft adaption - it was on the bottom of the menu for my version. Run it, open your throttle wide/fully open and let the software do its thing - which is it revs the motor about 4 times up and down in quick succession. After this process, turn the bike off and leave for 2 minutes. Upon restarting check engine light should be gone and the error no longer exits in TuneECU software.
Hope this helps.