Meh said..
I've had the same thing happen a few times and I think I just ignored the message and it kept logging.My Garmin battery went flat after I had a good 2 sec. Later I got a good 5x10 with the Motion. I'm pretty sure I couldn't combine two sessions from different devices with gpsspeedreader. I'm sure I have managed to combine two FIT files though.
I'll remember that next time and keep going.
My Motion had run out of battery so the watch was my last chance and I didn't want to risk losing the session. 🙂