Can you just disconnect the regulator? I've run my 016E without a battery. I've never run it with a battery. I don't think it will hurt anything but do it at your own risk as I am not sure.
My 016D has a charging system, I think. It runs the electric pump. See pic. Isn't that a rectifier and/or regulator next to the fuel pump?
The E has 24vdc systems for fuel supply and solenoid to run. I do not believe it needs 24vdc to make A/C output at the lugs, but I'm not 100% certain. the D definitely does not need the 24vdc to run or make A/C.
If the E runs okay without a battery then the existing rectifer / regulator must be working okay. However, it is very dicey to operate with no reference on the regulator such as a battery. The regulator must react and stabilize the voltage based on the use of the fuel pump and holding solenoid and as we know the fuel pump is pulsing away. So that poor regulator is trying to maintain the voltage as the load oscilates. The battery dampens it out and presents afairly uniform load to the regulator. Even a dead battery, probably not a super dead or shorted one, though..
Now having said that the regulator could be protected by turning off the input. And the engine will run if the speed control is made to operate mechanically, which is easy if the little black lockout device on the red shutdown lever is removed. The mechanical off on levers can be adjusted to get 60 hz in the mechanical non solenoid mode. However, without the electric fuel pump pushing fuel to the injection pump the system may have problems.
I did a test a while back. I had an L100 Yanmar out and bolted to a 2x10 with a Chinese ST generator running at 1800 rpm. It was belt driven and the engine was at 2400rpm. I used one of the facet pumps and the standard B fuel filter and drew fuel from a 5 gal can. I turned off the fuel pump as it was running and to my amazement the engine continued running. I let it run 20 minutes with the pump off then I pulled the hose and put my thumb over it. After another 5 minutes the engine finally showed signs of instability and quit running. When I released my thumb there was a lot of suction. Now I know this is bad for an injection pump, and I do not like having the possibility of air getting into the injection pump because air in the injection line can ruin the injector tip and even blow it off and then ruin the engine.
So, yes it is possible to run the E without 24vdc and all systems off. Is it good for it? No. Will it tolerate it? Yes but for how long? Maybe a long time.... I do not know. If it had a gravity feed fuel tank that would be very beneficial. Complete L100 fuel tank assemblies with filter and petcock are on ebay for $55.
