I had the same issue on this bike. I actually asked an experienced Honda mechanic and he said "whack it with a hammer"....How unique!
I used a nickel in a pair of vice grips to get the timing mark cover off after squirting with liquid wrench. The flywheel cover (larger one) was tougher. I had to liquid wrench and PB blast it for several days and then I took a brass hammer and tapped (not a whack) it on the face several times too. I finally got it off via a large screw driver without any detectable buggering. Once they were off, each had a ring of "gook" that looked like it had acted like a glue keeping each from turning. I wasn't the threads themselves. but various items that had settled into the groove/space where the actual covers seat against the case.
I think the key is breaking that "natural glue" ring that seems to seep into the seating area on those......and probably something more along the lines of a solvent would speed up the process that I'll use next time, and I'm sure there be a next time on one or more of my others!