Just out of curiosity, how much fuel do you have in the tank. I have read about problems with the fuel pump priming if the tank is below 1/4.

Beyond that, there are really only two possibilities. One is that there is a leak in the o-ring seal around the fuel filter cap, or a leak in the seal of the water separator plug. The fuel pump draws fuel through both of those, creating a vacuum there. If there were a leak, enough air could be drawn in to prevent fuel from being pushed up to the upper fuel bowl. It would have to be a pretty significant leak, I would think, to keep the upper fuel bowl from filling at all with it's cap removed. I think you'd see bubbles there with the pump running also.

The last possibility is that the fuel pump just coincidentally decided to go belly up right about now. It's a lot of coincidence but it wouldn't be the first time that's happened.

As an aside, I wouldn't be too concerned about vapor lock. First of all, diesel fuel's vapor point is well over 300 degrees. And second, the fuel pump is designed to be self priming. When you drain the water separator and change the fuel filter, the pump is left sitting in air. It has to have the ability to draw fuel in from the tank and push the air back out through the return line. In the highly unlikely event that fuel vapor developed in the pump, it'd be pushed out just like the air would.

P.S. If you really want to disconnect the fuel heater, it won't hurt anything. It's the wires with the brown plug on the fuel filter, separator, pump module.