Pre-fill is the answer. Over time priming pumps in canisters will only cause issues. The last time I used the priming button in one of my Eheim Pro II, it caused a leak. I needed to disassemble the head with the motor etc, and replace the gasket that is there to prevent leaks through the priming pump. The filter is now fine. Fortunately I had a spare canister on the shelf and was able to swap out the head until I got the needed gasket and replaced it.
Depending on the filter model, how much air can be in it before it wont restart correctly varies. There is a way to minimize this. I cannot say how it is with other brands and models, but the Pro II closes off the intake and return hoses when they are disconnected to clean the filter. The hoses remain filled with water. I wait until I have mostly refilled the tank with new water and then I reconnect the filter and open the taps. gravity does the rest and water flows downjhill though the intake hose and any air in the filter expells via the return hose. The Eheim has taps built in. If your filter doesnt have them, install two ball valevs close to where the water enters and leaves the filter. Close them both before removing the filter to clean it. When you return the filter and reconnect the hoses, open both of the ball valves and let the filter self fill. The more you fill it before you put it back in place, the better,
