I would avoid using MTR mode and bouncing on the H4N if you can. With just two tracks already recorded, upload them to a PC DAW as through they were a stereo pair. Use the DAW to split them to two separate mono tracks and then proceed as though you had recorded two separate mic tracks directly into the DAW. If you don't already have a DAW, you could download something like Reaper, which gives you a 30-day unfettered free trial.

If you were to treat the tracks coming in from the H4N to the DAW as a stereo pair, you would not be able to apply EQ, effects and dynamics individually to the two tracks.

Awesome, Thanks for your help, I'll give that a go!!