The way the fuel pickup works is a simple design actually.
The taller of the 2 filters pickup fuel when your riding around in "ON" mode on the petcock.
When you get low on gas, lower then the top filter can get at, the engine sputters,so you switch to reserve, which is the filter that goes right to the bottom of the tank. Think of you drinking a can of soda with a straw, and you cant to the bottom of the can because the straw is to short, so you get a bigger straw. This is similar, but reversed.
Fuel in ON position...
/forum/uploads/cdnninjazx6r/fuelon.jpg
Fuel in reserve..
/forum/uploads/cdnninjazx6r/fuelres.jpg
How the reserve would stop working I dont know, since its not actually a seperate tank, just a lower pickup. Maybe the reserve pickup had gotten blocked.