It is not advisable to ever pump without a filter with a positive displacement pump unless one wants to buy a new pump. One small particle will ruin the gear pump or lock it up.
Now with fryer filtration, the normal problem is a air leak on the suction line. Usually a O ring, but sometimes a crack in the line or a fitting, or a carbon blockage in the suction tube. I have also seen socket wear from insertion of the tube. Close visual inspection of the suction line is needed.