I have honed many a cylinder with pistons in place. Its more of a roughing up then honing, just a few laps around is all it takes. Maybe I have been lucky all these years, but I have not seen any problems. I figure all the turbulance from compression and explosion blows any remains out the exhaust.
If you feel this not something you prefer not to try, by all means don't, we all got opinions and are free to choose which ones we believe. I have done a lot of stuff over the years that you are not suppose to do, some worked some didn't.
Joe
