Newly placed fountries without any recipe selected are SA's original fountry. Foundries with molten recipes selected will be replaced by "fountry-molten". So if you connect a original fountry with something, then set its recipe, the entity will be replaced and the circuit will be removed.
I personally believe the code replacing entity triggered something that caused the desync problem.
For multiplayer testing, a quick solution might be downloading additional factorio clients, they can run at the same time on the same PC. Use one client to host (LAN, dont select verifying user identity) and another one (dont sign in, use a different random ID) to join.