Like I said, it just resets the current rep count. You get EXP every 10 reps (during the first half) and then every 20 reps (during the second half). Not sure if those are the exact numbers but that's the general idea.
So, if you do 25 reps of a move and then check the command list, you'll get 2 EXP points for that move because you did 2 complete sets of 10 reps each, but the last 5 reps you did will be thrown out and wasted.
You could confirm this visually in the DC version if you were a habitual progress checker.
Ah ok. So just don't go nuts with the checking of the list and you'll be fine.