Hi,I am author of "simple_water_rail_with_collision_rewrite",
now I realize it is because I am overrided the LTN train stop`s collision mask with extra "rail-layer" collision,so it block the combinator ghost and removed and LTN cannot found the removed ghost so it created new one,so you observed the wire connected is disconnected.
the fix is implemented in version 0.0.17,hope it could work with you now :/