I shot an interview with a Canon 5D and recorded the audio on Nagra 4.2. Should i convert the clips with HDlink and then import them in NLE, sync audio and re-encode? I'm afraid to loose a generation by compressing twice.

Or should i import audio and H.264 clips in NLE, sync and render to Cineform to have a first generation Cineform file?

Which software would you recommend?

I have been using Vegas for 4 years but just got Premiere CS4 and from what i read with Premiere you do not have the color space issues that Vegas has (Computer RGB to Studio RGB, Smart Rendering).

Is Premiere easier to deal with in that aspect where you just import clips and not worry about color space and other issues like that?

There are no issue compressing twice with CineForm, or 10 times for that matter. Why do you need to create a new sync file? Can't you simply keep video and audio sources separate in the NLE. Vegas doesn't have colorspace issues, CineForm works with their colorspace correctly, it just a matter of getting your mind around Sony's choice of black level.