I figured it out. I'm not sure if this is normal behavior for Logic, but it worked for me. I had sliced some of the audio tracks to apply adjustments to only those sections. I figured that Bounce AND Join would do what it says-- well it did -- but it "erased" my flex adjustments. Instead, I Joined first, THEN I bounced in place. Now my flex is off and the adjustments I had done previously with flex are still there. I hope this helps someone.