When you say you were unable to "get the primer pot to fill completely" do mean before you turned on the mortar or the mortar wouldn't fill it? Has to filled to the correct level or it won't prime. If you can't keep it filled that's where you start tracking down the cause.

I assume you have a check valve on the outflow pipe? They can fail. I don't know your system layout, but back flushes could clog something.

Lid on pot isn't sucking air? Gasket looks OK?

Does any water come out of the outflow pipe?

You can try forcing water into the pump. Stick a garden hose down the skimmer intake and fill the remaining gap with a rag. Prime pump, seal, turn on hose (best to have someone holding the rag in place as best they can. Then turn on the pump. If it gets going you can remove the rag and hose (with hose still on). You have to be careful, once the pump is drawing it'll try to suck the rag in and it can be hard to remove. So it's a bit of a dance. Using a huge rag is a good idea because if it gets sucked down the pipe hopefully some will be sticking out and can be removed after the pump is off.

If that works you'll know you have a leak somewhere on the suction side if you see the pot continue to fill with air, or you see air bubbles coming out of the outflow after running for say 10 minutes. Air bubbles for the first few minutes is of course normal.

You say it was working fine until you backwashed the filter. Do you have a bead filter? I would guess that you either have one of two different problems. One is the oring on the pump top is missing or filter is building air pressure. First take the lid off the pump and check and see if the oring is in place. If it is turn the multiport handle to filter position. Fill the pump with water and turn the pump on. On the top of the filter you should have a air bleed off valve. Open this valve and leave open until water starts to come out. The should be pumping water. If there is no air bleed off valve than loosing the nut on the union on the output side of the pump. Loosen this nut just enough to let air out of the union.

The next question you are going to ask is why did it happen and will it happen again? The answer is when the air blower was turned on it blew all the water out of the pump and yes it will happen again. Why did it just start happening? The gasket on the multiport valve is starting to wear out allowing air back to the pump. Also the check valve on the system is starting to fail. If you have a valve on either the output or the intake of the pump shut these valves when blowing the filter during the backwash procedure.
When the multiport valve gasket gets worse you will start to see water going out the waste line when the multiport valve is set in the recir position.

You might have an air leak on the input side of the pump as waterbug guy suggested but I doubt that it would suddenly show up right after backwash.
Mike