I'm new to PreSonus & mixing in general so consider this in that context...
I had a similar problem but had done some pitching of notes through the Melodyne connection. I can't recall if this fixed it since it was a while ago but I think I undid the Melodyne (CNTL+ALT+M) and was able to hear the changes. When I've had similar problems in general because I haven't learned the proper fixes yet, I have also mixed down what I had to a new track and then kept working from that point forward. That way, in the end, I can delete the start of the mixed down track and the end of the original track with the issues and combine them. Not pretty but when I've been in the middle of stuff I didn't really want to spend a tonne of time trying to discover what went wrong.