FreeStyle has an extra feature for playback loops called loop overrides. Loop overrides make it possible for you to make changes to measures within a playback loop without affecting the other repeating measures in the loop. For example, suppose you have a 1-bar drum pattern that is looping throughout your entire chorus. If you want to add a couple of fills here and there but leave the rest of the loop intact, you can just override the loop for the bars you want to change. In fact, if you just want to overdub your changes on top of the existing loop, FreeStyle will automatically make loop overrides for the measures that you record on top of.
