Sorry for the delay - wow, that scope looks like a bargain!
Well, I'd attach the scope across the mechanical counter, set up the trigger on it at 1.5v (50% of the signal) and then try running your code. Basically you're looking for reasonably straight edges on the signal as it goes from high-low and low-high. If you see the signal 'overshooting' and going up much above 3.3v (the normal voltage for the IO) or below 0v then you know that the inductance in the counter is pushing voltage in to the microcontroller, which is bad for it long-term. Otherwise you're fine
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