Thanks for that. Your mod is definitely going to be useful for some of my playthroughs, but it's useful to know I don't need it depending on what other mods I'm using.

The calculation of City Connections is tied to the player's first buildable Route, in the vanilla case being the Road. So yes, if you move the Road, the City Connection logic will follow.

Can I just clarify the nature of the problem this fixes. Is it the case that because Road building is unlocked at The Wheel, no city connections will be recognised before that? And, crucially, if I have a mod that changes which tech unlocks Roads, will the tech the connections form at change too, or does that need to be changed separately?

The fact you have The Wheel means that this mod wouldn't be having an effect on anything anymore, but I tested myself anyway and found it worked fine. City Connections have nothing to do with rivers or continual territory, my hypothesis would be that your two cities don't have a continuous revealed coastline.

Btw it was well passed wheels and harbor requirements and techs

So i had a game where a newly built city was founded by the coast far away from.the main territory, and some 6 or 9 tiles away, a small town already connected to the capital and with harbor did not connect to that new city sooo idk if it has to be only by river to auto connect the territory tiles first or usual both have harbors built first
Maybe look into it if you can

Neat.