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but it seems only two channels are available for users.
I am not sure this is an nRF restriction, this is why I am posting, so that Gordon and Fanoush will correct me :)
In any case, please run this to verify how many watches are running when you get the mesage that no more watches are available. Maybe some app is using a watch etc.
global["\xFF"].watches
I just tested setWatch with 3 pins (D32, D24 and D22 (found this pin additionally)) and confirmed only the first 2 pins with setWatch work. I don't know how many GPIOTE handlers are available in nRF, but it seems only two channels are available for users.