How is the session set up? If its Interleaved, then I'm not sure. If the session is not Interleaved, then its behaving as expected.
Just an opinion, but I don't see much advantage in going thru putting things back to stereo after splitting them. There's no sonic change. Next time, you could balance things in a different method such as, insert a dual-mono EQ and adjust the input(or output) of one side as needed(which could also be automated). Once things were re-balanced, you could use the Commit up to This Plugin option to render the change. Just food for thought
