I have audio recordings on tracks 4 5 and 6. Track 5 needs to be re-recorded as a punch in. Evert time I record track 5 and accept the take, track 6 disappears in that identical section of the song. I am stumped
Actually, Now that I think about it. When I was recording the other track the track below it would be highlighted with no data on it and I would have to delete it. This is what is happening here as well.

Check your Prefs-Audio settings.

If you are trying to record a single MONO track (5) make sure the option for 'Input Channel for MONO Tracks' is set to either Left channel or Right channel.
From your clues it sounds like you want to record the left and not the right. I assume left is 5 and right is 6.

So set it to Left only .. see if that helps.
This is assuming the tracks are MONO tracks, but that's the most likely scenario for this occurring.

Edit to add image

Yes, they are mono vocal harmony tracks. I will have to check your suggestion out.