tried sending him home?
he should appear at the ferrymans dockhouse (not the dogfood factory where you picked him up), but if you have him follow you again he'll bug out and just become "dog" (aka dogmeat).

No, I hadn't tried that. Thanks for the tip.

Here's a thing you might try (no guarantee, save first).
- Stand in an open space facing Churchill
- Open the console (tilde -key on English systems)
- Click on Churchill to reveal his ID
- enter the command "player.placeatme ID" where ID is Churchill's ID. It may even work without the ID provided you have selected Churchill.

He should now teleport to your position. That being said, it's been years since I last did something like that and I don't know if it still works or will work with Churchill.

Bumping this one because it just happened to me

So after leaving the ship the doggo was nowhere to be found. I explored a lot on my onw including locations that force an area transition, like the Greenwich Pindar, but the little guy remained absent.

I went back inside the ship, exited the ship and fast traveled to the Mitre and the little guy reappeared.

So churchill does exit with you , he is still there just underground for some odd reason he spawns beneath the floor and just keeps following you untill he teleports out.