I've had issues with this since Audio Track was introduced. It's great that things can be Normalised and Reversed, and the Clone/Make Unique does help. But I've noticed on some clips and cuts things don't stick when I reopen (maybe because I didn't Clone beforehand?) and/or one cut I reversed and cloned - all cuts of that bit are now reversed as well!
Just to be on the safe side VA, get the parts how you like them in OP to start.
But I would right click the reversed bits and such, open in Audio Editor and reverse and clean their ends and such and 'Save As - Reversed Bit' and reinsert into OP.
That way you know OP or yourself can't mess it up, and any nasty pops and offsets are taken care of.