Yes it will default back to Factory setting. You will have to run YPAO
again and change back any other settings you have changed, macros,learned functions, set up control I.D. etc. Yes it's a pain but so is Not running HDMI and or having switching issues. I am sure this other memeber(Adam) will guide you thru this. I have friend like that too he can pick up my remote and go thru the Advanced Set Up Menu like I turn off the Tv

Good luck hope you sort out the problem and post up how it was cured.