@flart Thank you for bringing this to my attention (and sorry for the month delay)
I can't reproduce though, using restock and restockplus part variant switching works as expected, so is probably the effect of another mod? I can see you have several mods unfortunately I can't go through all of them but I can make an educated guess... I would check the mod that adds that "RCS Mode" bar if is the cause.
It does, but probably isn't hooked to the event the mod is firing when the variant is applied, currently RCSBA just listens to the ShipModified event since that should cover everything, but perhaps the mod is using the VariantApplied event without firing ShipModified as well. If you can pinpoint the mod I can check. It should be an easy fix although if my guess is correct then the problem is that ShipModified isn't being fired.
Edit: I can think of another issue that could be happening... so for a fix I really need a minimal mod list that triggers the bug.