Hi Ryan,
We were filming a shirt film yesterday and had this same problem. We were also using the same Tascam recording in dual mono. Our DIT transfered the audio clips, but somehiw they got deleted. Were were able to recover the files with an SD card recovery tool, butthey play the exact same way.
I know this post is two years old, but did you ever find a way to resolve this problem without cutting the track into tiny little pieces?