"cleaning mode" is just frying everything to carbon with crazy heat.
I doubt visible flames are good in much of any way, as flame can be much hotter than ovens can tolerate. The byproducts of flame from even just food are vast and many are cancerous, too.
Regardless, you'll have to clean out the soot and other products of combustion, or else you're eating many things not even open fire could reduce past toxicity (which is a lot of things)
"self-cleaning" isn't about magically being clean, but about reducing most things to soot/smoke, which can easily enough be wiped up/vented.
It's about making cleaning easier. Not about literally being "self-cleaning".
To recover from this, just clean all surfaces within the oven thoroughly so there cannot be any unwanted byproducts in future endeavors, and you'll be fine until next cleaning time.