So, quick update.
I went to the dealer today. The CEL was lit when I left home, and after I did a stop on the way, it turned off before I reached the dealers repair shop. Not saying I want it to be lit, but that was bad timing for it to go off. The mechanic believed me though, however he never saw the problem before and could not tell me anything more about it. They also only sold ten Zero SR F, so I must be in the unlucky ten percent.
Hopefully CEL warnings disappearance is permanent, and perhaps some condensation still left finally dried up from inside. But the warning light went off before and then came back, so not super optimistic.
I checked the console, and since yesterday I got error 31 (Battery Module Ineligible) and error 43 (Isolation Fault).
The dealer said they will need four weeks to even look at the problem, and do not have any loaner bike service. So, that sucks. Doesn't help to have a good warranty with Zero if the dealer put you in a long queue before acting on it.
I guess I will just keep driving it while waiting for someone to check it, and hope for the best. If it doesn't break down before the winter, maybe I can just have it taken care of in the off season... Kind of disappointed though, one worry I would not expect from a MC that is advertised as nearly maintenance free.