Thanks for replying, Mark. If the Apple ProRes had been around when we started this whole mess, we probably would have just started with that to begin with. But we are where we are, so I have to deal with it.
Yes, I realize all to well the problem that is conflicting frame rates.
I guess the way I should have put it in the first place is: we want to mirror all of the media we have, which is now NTSC, in the new HD format (I believe we're going to capture with Apple ProRes as opposed to DVC ProHD).
We want this transition to the 23.98 footage to be easy, but I know there's no way that's going to happen. We have a ton of subclips (I know, subclips are evil) and I'm afraid that those subclips are no longer going to reconnect to the new HD material because of the different frame rates.
One idea I had was to lay each clip (or subclip) from the browser into the timeline, run it through Cinema Tools to remove the pulldown, and capture the HD footage from that.