I'm going to be flashing a 2020 R1 for the first time with Woolich Racing, I asked support about it and this is what they wrote: It isn't possible to read the ECU out, but the files in our software are all original factory maps anyway, so you can always access the stock maps when you need to. Having fault codes shouldn't prevent you from flashing the ECU, however the only way to remove those faults is to first plug the AIS and O2 sensor back in, clear it with our Diagnostics, then you can Disable them in Advanced Settings, then flash the ECU. At that point you will be able to remove them again without fault codes appearing, but you have to complete those steps in exact order.