How long has it been since you've changed your fuel filter?
I'm not sure about this type engine, but there might be some "wicks" (sensors) in the fuel filter canister/housing that detect the water in the fuel. Those might need to be cleaned. A lint free rag (baby diaper) would clean them as well as you could. Don't use paper towels as that might leave lint in there.
Is there a dump that would allow fuel to dump out of the fuel filter canister/housing? If so, it might be a little lever to allow the water/fuel mixture to dump out of there.
I bet it's something simple, like your fuel filter needs to be changed.
I'm not a guru on Chevy diesels, especially the old 6.2, but I'm sure someone in here would have some other ideas.
Jordy, any ideas?