As long as the ECU is still the same ECU the AccessPORT was installed on, it doesn't matter that the engine was rebuilt.
If you want to be 100% sure, you will need to go a little further to verify the AccessPORT programming is still on that ECU. With the engine off and the key in the 'On' position, go to the Tune -> Change Map option on the AccessPORT. At that point the AccessPORT will look for its data on your ECU.
If you get to the next screen where it asks you Realtime or Reflash, you are golden and you can cancel out and no harm will be done since we haven't started doing anything yet.
If it comes up with an incorrect vehicle error, then that AP's data is not on your ECU.