I haven't, but it would be difficult to question the input pins being functioning, since I do get the encoder readings in a fair enough manner, it is just that there are missed pulses which is not adequate for my application of precise distance measurement.
With the latest code I posted, there are on average 3 missed encoderCount pulses for every 4 revolutions of the of the encoder. This is pretty much consistent and only in one direction.
I have an Arduino Nano Every somewhere, but since it requires soldering I haven't opted to try it instead.