Separating audio from Dual Mics

So I recorded some interviews with my Sony HVR-V1U (I've only had it a couple weeks). I used a shotgun mic in Input 1 and a lav running to XLR Input 2. I had the Channel Selector on CH1. I thought the way it worked was that I could record with the handheld or lav mic from one XLR input and the shotgun mic for backup then completely isolate the two in FCP. I assumed A1 in the timeline was going to be the sound captured from input 1 and A2 from input 2, then by simply muting one or the other I could get isolate the closer mic, or adjusting the respective volumes I could get a nice mix.
The shotgun mic picked up a lot of room noise but at the time of recording I wasn't concerned abou that because I thought I'd be able to eliminate that track. Now it seems that the audio from the two mics are mixed together so I'm wondering how to isolate the audio track that I got from the closer mic, if that's even possible at this point. Did I irreparably mix the audio from both mics?
I hope I provided enough info. Thanks for reading.

...and I did have my XLR Set on 'Separate' and not 'Linked' in the camera's menu.

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