but if I go back to using NiMH it means I need to unplug the Smart Stop?
Absolutely! NiMh has far more voltage drop than lipo and you'd be lucky to get a few min running with NiMh before teh smart stop would trigger and it would keep triggering to the point you couldn't get much running.
NiMh is run with no voltage cutoff. Even escs that let you run both tell you to deactivate any lvc when running NiMh.