When I restart mine, I restart HA only, and all of the add-ons (including NodeRED) keep running. The problem is as soon as HA restarts, it blasts all of the states to NodeRED, and for the most part (I think), they all go from "unavailable" to "on/off". This restarts whatever timers NodeRED keeps track of. I don't know of a good way around this, but I restart HA so infrequently that it doesn't matter for me.