If you run totally dry, I wouldn't count on a filled fuel filter to start the engine. Having some experience in this area, here's what I did. (This was a planned event--I wanted to know how many miles between fuel light and flameout there were.)
Put a couple of gallons of diesel in the tank from the emergency container in your trunk, something that we all carry.
Put a vaccuum pump on the return hose from the fuel pump (the one that runs from pump to filter and is not see through plastic) and pump until you see fuel travel through the plastic tube running from filter to pump. This takes a while.
Crank the engine for a few seconds. Even after flameout, there will be enough oily diesel in the pump to keep it lubricated for some amount of time. Don't know what it is, but I believe it is longer than you think. (Mine did not start.)
Reattach pump and do some more pumping until you can get a drop of fuel out of the return line of the pump. This takes some pumping because now you're trying to pull fuel through the pump and not just air.
Crank again. Mine started.
If it hadn't, I probably would have cracked a fuel connector pipe nut, but I didn't have to.
Good luck