If the footage was shot at 24p, you can remove the pulldown in AE to create 23.976 footage:
If it's truly 29.97, you may be better off using a third-party plugin like Twixtor to do the frame rate conversion.
In either case, it would be best to transcode the footage to a lossless codec prior to importing it into AE. I personally like Quicktime movies in the PNG codec.
When it comes to audio, the result is acceptable to me, but I'm not an audio guy of any sort.
When it comes to video frames, it depends. Normally it's easier to go from 23.976 fps to 29.97 fps than in reverse: some extra frames created either from duplicated ones or pulldown are unnoticeable in most cases or even preserve 'film look'. When you go back, you have to decrease the amount of frames, and that can be done with several options:
- drop frames;
- frame blending;
- motion interpolation.
The latter one gives the best result, whereas involves hardest work. So, what may that mean? E.g. the following: if you're not happy with in-built PrPro tools for handling frame rate conversion, 'Hello, Timewarp, my old friend!' See this good old tutorial from VideoCopilot on frame rate conversion and how to simplify your life with expressions (Andrew breaks down the trick at the end).
If the PPro 23.976 timeline is progressive then what you want to do is introduce 3:2 Pulldown in your AE rednder Cue. This will give you a comp that's the same length as your original. It's the same thing you do when you transfer film to video except in reverse.
What ever you do don't re-interpret your footage from what it is to something else unless there are no sound sync issues. You must know exactly what the footage actually is and know exactly what you actually want before messing with anything. Unfortunately I only know just the basics about your footage and your PPro project.
If you just drop the 29.97 fps footage in a 23.976 comp the speed will be perfect and AE will adaptively blend the frames to give you a pretty good result. The best option is based completely on the kind of shot that you have. No matter what you do there will be different motion artifacts. Generally, if I'm faced with this kind of problem I just re-render a production master by adding my 29.976 comp to the render cue and then change the output settings to add 3:2 pulldown. The rendered file will be in sync with the sound and at the right frame rate. This will give you 23.976 I footage which should work just fine in your PPro project unless I don't know something about the PPro project.
If something is different thatn I suspect then everything except not simply changing the interpretation of the footage may be incorrect.