I used to record to twin R-09s all the time. After transfering the files to the computer I found needed to stretch one source in addition to sync'ing the two for recordings of significant length..
However, I would also often playback the recordings direclty from both recorders simultaneously, manually sync'ing them at the start (a tricky learned skill requiring patience!) and they would then playback in perfect sync until the 2GB file split. I surmized that the timing differences between the clocks which were encoded in the recordings were compensated by the very same clock differences on playback. I never swaped cards between machines before playback to see if the timing differences between them doubled instead of canceled out, but that would have been an interesting experiment.
That's not much help to you, but I thought it was pretty interesting.