You can add a ship to a control group using ctrl+shift+N, and it will add those ships to control group N even if there are ships in N that are on another planet. Thus, the old ships won't be replaced in that control group.
That said, now that all ships no longer get an energy use reduction in stand down mode, there is no reason why any auxiliary support effects should toggle with it. Only attack, repair, constructing, assist construction, gravity, self-damage to regen allies (regen golem), self-degeneration, and tractor should toggle with stand down mode. The rest (notably including, but not limited to, boosting and tachyon beams) should stay on.
This would also help out eye bots, btw.
(Speaking of repair and assist construction, I have another case where engineers will try to assist something it can't repair and can't help construct something anymore. I'll post a save in a new bug report tonight tomorrow)