Chewtobacca said:

It won't. I understand what you are saying about not wanting anything to be altered at this stage apart from the color, and that's fine, but you shouldn't apply RFF flags to 29.97fps video. At some stage, you will have to slow it back down to 23.96fps and then encode with RFF flags i.e. apply pulldown.

This. ^

Ideally, what I would do in this case is use another tool such as AviSynth to interpret the footage as 24000/1001 progressive and save a lossless master. IIRC, DV/DVCPRO supports neither of these things, so it's at best suitable as an intermediary.