Speed regulator parameters might be adapted, if a 3hp VFD regulator is "too responsive". You will get a feeling of your speed regulator setting, if you take speed regulator output, typically called "torque reference" or similar on some kind of internal high resolution trending channel or track it via a D/A output with at least 1ms scan to an oscilloscope. If it is too "volatile", the curious sound you hear might be the wear out of the coupling between motor and fan.

Has anything changed with the installation? 3hp VFD parameters adjusted, mechanical adjustments, etc.? If so, that would be the first place to look. Can the noise be isolated to a certain part of the system (motor, gearbox, ID fan)? Noise caused by potential bearing issues can often be simply identified by a stethoscope (or by "listening" to each bearing using a long screwdriver, but there are too many safety issues for this method).