If the fan has been running without noise issues by variable frequency drive it is likely bearing fluting caused by shaft voltages. Most larger 50/60 Hz motors suitable for inverter duty will have the ODE (Opposite Drive End) bearing as insulated and will use a shaft grounding options to bypass any stray voltage, common mode coupling, static voltage on the shaft to not pass though bearings.

Those darn insulated bearings and shaft grounding devices always end up causing problems as they are commodities and need attention to keep them functioning properly. I wonder if the 5hp VFD is being used and what level output topology the variable frequency drive produce?. Why would the 5 hp VFD be operating in Vector mode when applied to a variable torque fan load? In theory it should not make a difference but scalar (V/Hz) would work just fine. I once had a submersible pump (motor surface mount connected via a shaft) that just did not like Vector control mode.

If the 5hp VFD is over rated for the ID fan load you can simply increase the carrier frequency provided it's not already beyond 6k Hz. The skip frequencies can be implemented, however depending on the control scheme might not work for your application of GoHz 5 hp VFD.

VFD (Inverter) converts AC power to DC power, the DC power is switched with either IGBT or Thyristor to construct a quasi-sinusoidal waveform. This is done by pulse-width-modulation (PWM). The PWM changes the voltage level and duration. IGBTs are the most common switches used in VFD. IGBT has a mosfet driver, it can be controlled at high speeds. Thyristors or (SCR) gate are held on until the current crosses near zero. Actually, the dc is never converted back to ac. The output of 5 hp VFD is pulsed dc (380 or 760Vdc); Pulse Width Modulated - PWM. Put a good digital voltmeter on it and see. The motor is very tolerant, though.