How can I drill a big diesel tank without emptying it first?
Seriously: You just don't.
Reasons:  


You'll never be able to guarantee you didn't contaminate the fuel unless you clean it thorougly after the work, which you cannot with all the diesel in there. That bears great (financial) risks. If you sell that stuff you might even get sued. Special drills and precautions will surely reduce that risk, but it will still be there.
Any hole added after the tank has been varnished / coated damages that layer and the walls of the hole are naked as well. That is a starting point for corrosion. There is a reason coating is the last thing to do in such constructions.
Finally: Would you rely on statements such as "Diesel has a high flaming point" or "use argon on the empty part, to suppress fire"? With your Life? Really?! If someone told me to drill into so much as a tin can filled with diesel, I'd tell em to have fun trying themselves. In you case 3500L. Obviously Diesel is not an explosive so the effect is different but just for the giggles I did some math: The energy in that tank is equivalent to about 340000 kg of TNT, yep 340 metric tons.


Solution: Hire a professional to do the job.
They know what they're doing and they bear the risk and liability.
There's a reason they're called professionals.