I am not quite sure about the issue you are describing. How are you determining that the fuel filter is not staying full? Does the engine run or are you chasing a driveability issue or no-start condition?
I will assume that it runs and has a lack of power or other running issue. I like to look at the simple things first. Based on that, I would say that the lift pump (not the injection pump) that brings the fuel from the tank to the injection pump is weak or is allowing a back flow to the tank. The other possibility being that the fuel line and or a seal is sucking in air and the diesel fuel is becoming aerated.
If you can provide more information I can be more helpful. Thanks and good luck.
Seeing how smarter minds haven`t answered yet. I would guess it`s air somewhere in the system, like a line not tight or a crack so it sucks air. Maybe squirt soap and water on lines to look for bubbles or air movement on lines, filter, pump? Some clear housed filters (probably not yours) fill less and less as they start requiring a needed change. Good Luck