Unfortunately, there is no any way to remove attributes without damaging the variation connections and I guess we can do nothing here.@Yaros
Thank you, but that's a serious thing and I think there should be some warning. I've got a lot of work to do now.
Is there any way to hide certain attributes without hiding all of them? I don't want the shipping location or seller's name to show, but I do want to show things like material.
It would be great if this were addressed in a future update. I'm no expert, but I don't see how deleting a variation can break updating stock count and prices.