What would cause a power meter to report negative vars?
The peculiar readings may be the result of harmonic currents drawn by the VFDs. You need to investigate how the meters show that. The reactive component of the motors that are powered through VFDs is supplied entirely by the DC bus capacitors in the VFDs. The current supplied to the VFDs has a substantial harmonic component unless they contain harmonic mitigation provisions. The current for a system with harmonic current content has three orthogonal components, X representing the real component, Y representing the reactive component and Z representing the harmonic component.

You should determine how much of the motor load in the facility is due to motors powered directly by the three-phase power source and how much is powered through VFDs. Also determine the harmonic content.