When using "Sharing->Overwrite Existing Web Layer" from Pro and the new layer happens to have a different Layer ID than the one it's going to overwrite, there NEEDS to be some sort of routine that automatically checks all WebMaps to ensure that none of them will "break" and at the very least give a warning. Ideally, there should be an option in that warning to automatically change the layer's reference in any WebMap that references the old layer's ID to match the new layer's ID.
Yes, I just discovered that layer IDs played an important role and that moving their position in Pro's TOC changes its ID. I publish all my layers individually from a Pro "sandbox" project (contains all my layers) and create/author all my maps in AGOL.