Hadn't thought of leaving water in to add weight.
I generally drain it and then pull the rod.
When I flush it, I let it drain completely first, then with the valve open start water back into it. with the temp setting turned to the lowest it lets me.

Then I let it run like that with the relief valve shut to build up pressure.
I let it run like that for a few min, then shut off the water to let it drain.

typically towards the end I see pieces of the old rod coming out. So I pull the old one before I do it, because chucks come off.
the first time I pulled it, parts of the rod had swollen and it wouldn't come out. so it really broke off large parts getting it out.