I've noticed that one of my devices is sometimes losing WiFi connection and is unable to reconnect again. I've updated NONOS core first, but still - same problem. Another ESP8266 based device with same code worked without issues.

Why?

Because of... RF_CAL (RF calibration area). This area isn't cleared automatically with every OTA update or serial flash - by flashing various software (with different SDK version) you might end up with incompatibile SDK in context of RF_CAL contents. That's why it's recommended to erase chip.

Doing full chip erase and then flashing software fixed the problem :)