More likely a bug of the game, have you reported to UG first?
Not yet. I will do this, but I think it is not a bug, but a safety precaution. Sometimes you want to keep things unchanged you have built before. Imagine - it will change everything on the map! If you don't notice some perhaps unwanted changes, you will save your map and perhaps you can never undo them. I once had a problem with VacuumTube's slope mod. If you don't deactivate a special checkbox, the update of some streets in mountain areas will destroy whole mountains. If you do it manually, you notice this. If you would update automatically, you would not see it, and your savegame could be destroyed forever. I myself know that global updating is a very risky thing - that's why I will be very careful with my update mod.
But I think something like a special update key or menu would reduce the risk.
You may keep the nodes from construction side and rebuild edges from free side and using the nodes from construction side so they should get connected.
You always have the same idea like me. But what about two neighboring constructions?
What about "asset/wk_switch_kit_de_at.con"
I could send you a pre-version of my update mod, so you could make your own trials - if you want.