Interesting.. could you try disabling the experimental setting from this mod (it should be the only setting under Redrawn Space Compatibility).
It's possible that route removal logic is a bit too aggressive with the current numbers. That setting is only supposed to remove routes when the alternative routes are nearly parallel to the route in question, e.g. A -> B -> C appears visually similar to A -> C, so we remove A -> C
It doesn't look like it should apply in that situation though.