I ran into this type of problem on some generic controller, though I don't remember which one now. Never found a solution for it, but you're right--there should be some way for it to "remember" the setting.
If it is a wire you jumper to make it sensored vs sensorless, then that should always just work.
But if it's a "learning" wire you jumper just to make it learn the phase/hall combination, you can't leave it connected, so in that case it should remember it. if it doesn't, from the very beginning, I guess it's a design flaw. If it did at first and stops remembering later, it sounds like a failure of the controller, that might be fixable, or might require replacement.
If it only forgets when powered off it might be inconvenient but livable, but if it forgets while actually riding, that would need repair/replacement.
If it is a learning wire that is jumpered to make it work again after powering off, you could just add a switch for it, somewhere conveniently located for where you can lift the wheel to let it learn and then start your ride.