I have run a tank dry on the Mooney as discussed above. It took about 30-45 seconds before we had normal flow again. This is no big deal at safe altitude.
I recommend starting the engine on tank A, doing taxi and runup on tank B and not changing tanks again until at a safe altitude.
Also if a tank was run dry, just filling it up will not get rid of the air in that part of the fuel line that sits beween the tank outlet and the fuel selector valve. That air has only one way to go and engines don't run to well on an air/air mixture.
On the Mooney or Beech this part of the fuel line can be drained only if the fuel selector valve is moved to the right position.
On all these checks, it helps if the pilot remembers WHY he is doing it a particular way rather than blindly following a checklist.