While I am familiar with Premiere, I'm quite new to AE. I was trying to convert 23.97fps to 29.97fps using the advanced frame blending (thanks to the help of a creative cow podcast). For some reason after exporting, I'm getting what appears to be a 2-3 frame patterned-wipe between each edit from my original done in Premiere. I have a feeling this is something rather basic, but thanks for any help you can give.
i'm not familiar with the tutorial that you mentioned, but if it is using an effect like timewarp, thre may be a setting for scene change detection or cut detection or similar that may help you out here.
you may also be able to split the clip at each cut within the main comp and continue the process. you can split a clip by positioning the cti at the point of the cut and then hit command-shift-d.
worst-case you'd need to split the file into multiple comps, do your process and then reassemble.