How do I consolidate all project files to zero in my session?

OK, what exactly do you mean by "consolidate the session files to zero?"

Do you mean bouncing the track as single files/stems?

And if this IS the case, you need to go to File/export/all tracks as audio files.

;0)

Try this. I just did it and it worked. Make sure your playhead is at 1 or 0. Wherever they start from. Then go to file> export> all tracks as audio files and put them in your bounce folder. The open a new to project to check it and drag the bounce folder in and they should line up fine.
good luck and let me know how it turns out
Bart

To continue on bartwalsh's answer -

You can use the new feature - Export all tracks as audio files. This will do the same thing as consolidate in protools upon export although the regions within the logic arrange window will not be joined. All the exported files however will start at measure 1. One caveat I discovered - whenever I had a region of anything, midi or audio, muted or hidden, before measure 1 logic crapped out on me. Once I discovered this I moved everything a measure and it's worked well.

The old way is - create a blank bit of audio to place on each track at measure 1. Then select each track individually (which will select all the regions) and select Region/merge. This is quite noodley as you have to do it track by track. It's what I used to do when I had to export to pro tools.

Hope this helps.