A couple of links to my music... Thanks for listening.
YouTube Jon Brooks: https://www.youtube.com/jonbrookscomposer
SoundCloud: https://soundcloud.com/jonbrooks-1
This isn't as easy as it should be in Logic Pro. There are work arounds but usually I've bounced down the audio, taken the stereo file to another editing software and then bounced down a mono file.
I'd be tempted to adjust the velocity in the piano roll for any notes that need decreasing/increasing in volume. A compressor or multipressor would also help to soften anything that sticks out too much.
It's possible your original project could be corrupted. Have you tried creating a new Logic Pro session and importing all the audio tracks, midi tracks, content and automation into the new session? Best wishes, Jon.