Okay, so I purposely gave myself this "bug."
If you wait too long to go to Jake then Jake will wander to you. (Whih is easy to have happen since you are distracted by building in the settlement.) I have had him wander to Sanctuary and this time I did Red Rocket. This can also happen later with Hub of the Problem.
How to fix it without console commands:
I went and waited in the church at Concord for an hour. Jake kinda came closer.
I found Jake in one of the alleys doing the animation he should have been doing at the terminal in his shop.
Walk up and talk to him and then immediately run away, then Jake will start following you.
Run back to the Concord workshop and watch Jake as he wanders to you. Once he arrives in the workshop engage in the conversation.
Old Paul should come running in at that point.