I could probably handle an accel/decel curve at the pause/reversal, but the AXGEAR looked like it started losing track of master counts which was making the follower position move outside of it's prescribed travel limits.
Any change to the gear ratio can do that. It's inherent to changing the gear ratio. We do things to mitigate it, but that's what you're bumping into. AXGEAR is fundamentally a velocity relationship. It's built on a function that uses position, which is what the re-normalization process is designed to work around.
AXFOLLOW is position-based. That may not help you either, but it doesn't lose position but neither can it change gear ratio.
I can't help by think you might need a combination of these instructions. Rather than yanking the ratio around, explicitly build the behavior with states, maybe a combination of AXCAM and some moves.
At the very least you are outside the design intent. That limits my options.