Ahhh, I see what's happening. The connection name never changes from "nauvis-muluna", which causes the script to trigger, removing the connection based on the name alone (nauvis located on the inner side, muluna located on the outer side), even though the target/destination have been modified.
I can fix that issue to retain the connection, but this situation still isn't exactly playable. With the bare minimum, the only outer planets are Aquilo and SSEdge, both of which require inner planet sciences to research. The asteroid belt only requires the four base sciences to be researched, but it also requires the rocket turret from Gleba as a prereq tech, so there's no way to get to the inner planets, regardless of the connection.
Fixed in v1.0.29, but you're definitely going to need a third-party mod to deal with Asteroid Belt + Any Planet Start compatibility (when starting on an outer planet). There is fundamentally no way to go 'the other way around' through the Asteroid Belt, without modifying the Rocket Turret prereq tech (it is required for a reason).
