The easiest options are (1) generate a new traveling library every time you pass the document back and forth; (2) Keep two libraries. the second option is the preferred method for many of my reasearchers. For the latter, each collaborator needs to make sure she/he passes on the most current library (including associated .data subfolder). I have instructions for these options at http://chemistry.library.wisc.edu/writing/endnote.html#collaborative-writing.
Emily