I have a 294MC and so far I had the automatic debayering disabled and I could make flats with automated flat function in Ekos setting 31000 ADU and 4 second automatic duration with a dimmable led panel.

Yesterday I enabled the automatic debayering for seeing color images in preview but when I started making flats, with always 31000 ADU as target, the exposure time ramped up to over 15 seconds and whas yet to 15000 and I stopped it.

Now my question: what is the correct way of taking flats? I suppose to have debayer disabled and have 4 sec flats

You are still capturing RAW images, debayering does not have affect on the captured images. The previous way you were doing it is correct.
But it seems that there is a bug in Ekos for the automatic flat capture function. Next time I will capture flats I will try the second approach (i have the same camera as you)

Ok, let me know, I'm curious! It also happens that if I use the automatic dark flat generator after the flat shooting the dark flat shooting fails after the 5th retry, so I have to delete the dark flat sequence and manually add a dark sequence with leght determined by flat: does this happen only to me?