You don't say which mount you have, but in general the mount doesn't know guiding is taking place (think about it--if the guider is paused or the guider is issuing no corrections because tracking is perfect, how can the mount know the difference?).
What I think you are describing is that PPEC restarts after a slew. This does not affect whether you choose to guide or not. PPEC makes guiding generally easier and allows for longer exposures, but doesn't require, assume, or validate guiding.
Bottom line--stop guiding and restart when you want to. No worries.