we have just gone through this process in work here, and talk about a PITA!....
eTransmit was mostly harmless, bar the duplication of a few xref's, but we were able to etransmit the entire job as one batch and seemed to be fine, though it did take an eternity to pack up!
try it on a small job first and unzip it to a different drive....
Good luck....sounds like youre gonna need it!