It would all depend on the stone you were lapping with, it would be possible to polish a ceramic stone to the point it wouldn't cut at all. I'm using pretty course diamonds and it does leave a scratch patten, but I don't see it as a bad thing. basically the way I understand it is you want to cut the top layer off of the stone, revealing the new sharp abrasive. As opposed to a soft water stone where there is a constant supply of fresh abrasive as the stone wears, and the lapping is to preserve/ achieve flatness.
It could be that you are lapping with too fine a medium?