On my system, if the handheld controller gets unplugged, the commands that were input at the time will remain in-place when the controller gets plugged back in...until I undo what I don't want (I think this is so you can move the controller to a different jack without interrupting anything?). In other words, if a loco (any on the track at the time) was set to speed step 1 and then I unplugged the controller, the loco would return to speed step 1 every time I turned the system on, but not until I sent at least one (any) command to that loco. This would continue until I set that loco to speed step 0 and then unplugged the controller again.
...this is how I (currently) have programmed the numberboards on my SW1500 bashes since the Zimo decoders are set up with the extra function outputs on F1 and F2. Since the F2 function on my controller is non-latching, I hold down the F2 button and then unplug the controller. Now, every time I turn the system on, F2 will activate continuously any time I send a command to that loco and I get continuously-illuminated numberboards (until I hit F2 again) without doing any function re-mapping....which I my eventually do as my system does not store more than I think 6 locos' info this way.
...I should also mention that I've experienced a few occasions where there was a brief hiccup or something in the system where my controller behaved as if it was unplugged and then plugged back in, resulting in these seem frozen commands that I mentioned without having intentionally unplugged the controller.
