[Matthew Lewis]

I had the same problem and seemed to figure out/get help to solve this.

1) duplicate the problem footage in premiere by right clicking then clicking “duplicate”.

2) if you notice, the audio of the messed up clip is correct. we want to use this, so input the messed up clip into your timeline. after it is in, hold “alt” then select your video portion in your timeline. delete this and leave only the audio. move this audio only portion down one step into the “audio 2” portion of the timeline for now.

3) now, right click the duplicated clip from step 1 above. find “interpret footage” and make it 29.97 (or whatever FR you were trying to record in in the first place). now input this altered footage into the timeline. if you notice, the audio in this altered footage is now too fast, this is why we did step 2.

4) finally, hold “alt” and select the AUDIO portion of the altered footage in the timeline and delete it. move the audio from the messed up clip (which should be in audio 2 right below) and place it under the altered video footage that you just deleted the audio from.

Everything should be perfectly aligned now. I’ve noticed minimal errors aside from the occasional stutter when editing (doesnt show up in the exported final product), and lack of cooperation with twixtor (additional software for super-slow-mo editing)
hope this resurrects your footage man. let me know if this works for you as it did for me! (i’m using cs 5.5 btw)