Generally speaking, if the system is losing flow, there are a few things it can be. In their simplest form, 1) something may be impeding the output, 2) something may be impeding the input, 3) the system may be taking in air, or 4) the pump may not be moving water.
#3 should be easy - loosen the bleed screw on top of the filter canister when the system loses flow, and check to see if you have a lot of air.
1 and 2 may take some creative investigation, such as opening some hose connections to see what happens. Check the little hose underneath the unit between the pump and the filter can, too.
If it comes down to #4, for example, the impeller slipping on the motor shaft or some other motor problem, then naturally, you need a pump.
So we're back to your original question... when to throw in the towel. If the warranty folks are expeditious in their repairs, you may let them pursue their course until they change the pump, or you may be able to convince them to just get a new one and see how it does. You may even be able to replace the entire unit from ebay or Craigslist for less than the cost of your time.
I don't know if any of this helps you or not. Troubleshooting is a process of following symptoms and eliminating them until the root problem is uncovered and repaired. Sometimes it's more of an art...