Not sure. I just tried various ways to make it
not work, and didn't encounter any problems. If you can hear the effect of the live Arp right before bouncing, and you're bouncing the clip in the correct track, it should work. The only thing I can think is if you've previously bounced some other separate clip in that track, that will automatically turn off the Arp, and you'd have to re-enable it to bounce another clip.