Ok, I'm a Protools guy, so this may or may not make sense in Cubase.
If you can select a timeline to bounce to disk (like you can in Protools), then select from your zero mark out past the end of the song. Solo that track and bounce. Solo another and bounce...until you have them all. (If you can do a 'consolidate' like in Protools, that might be better; then just go fish all the files you need out of the project directory).
The point is to make sure all the tracks you transfer start at the zero mark on the timeline. If you have a track that doesn't start at zero already, just bounce the silent space in between zero and the start of the track. In fact, bounce *all* space, silent or not, between zero and the end of the song. It will eat some space when you're transferring, but the Protools engineer can take it out later. It's only a placeholder.
If you get them all at *perfect* zero (not even zero + 4 samples), the Protools engineer can rebuild the project using only the audio files, and you'll never know the difference. He'll import and drag them all to the zero mark, then it's like you never left Cubase.
Just a note - when you export or bounce, try not to affect the audio files *at all*. Eliminate all effects on each track and the master fader(s). Bounce to the same bitrate and bitdepth that you recorded in. (if 24bit 44.1kHz, bounce to 24bit 44.1kHz).
