"Yes-clean" flux has absolutely been the cause of controller malfunctions due to its conductivity for makers of my controller project. It needs to be removed.
Could be so, and it can depend on the flux and the processing, but it's almost never the flux. From a 10,000 ft look at your project, I wouldn't expect it to need the high isolation or high impedances that would drive a serious cleanliness spec. You could have other issues that a temperature and humidity test would uncover with no-clean, for example. We can discuss them if you'd like.
Depends on what you mean by "yes-clean" though - "water-clean" OA flux must absolutely be cleaned - it can start to corrode overnight even.
The "yes-clean" flux I'm talking about is high-solids rosin flux that leaves a conductive residue. The conductivity can definitely cause a circuit to fail.
Makers come to our discord chat, asking why their builds aren't working and post a pictures.
I suggest cleaning the flux off, and they start functioning.
As an aside:
My current solder brand (Chip Quik) has a "no-clean water-soluble" flux that I'm curious about. Surely that's not going to be as corrosive as the flux you're talking about. (I probably wouldn't use it myself because it needs 140°F water to dissolve)
Without answering how much conductivity you had, how it caused the circuit to fail, what part of your circuit failed, and in what way, you haven't really narrowed it down to the flux, even if cleaning helped. There are a number of more likely root causes of the kind of issue you describe. I can make time for going into that if you're interested.
"No-clean water soluble" is news to me. Don't know if I'd trust that in a humid environment.
But yes, no-clean flux is best left where it is.