I would definitely try upgrading your terminators to the Capacitance resistance type. See what the waveform cleans up to when you look at the system.
How far away is the closest LON Card to the chillers?
What Brand of chiller is it Reliance makes the refrigerant cooled VFD that Trane and Carrier use. As for a York I know it is a design of their own and there are many options to what filters and mitigation devices are included.
TCI is a company that makes EMI-RFI filters to be added onto VFD's that generate high frequency noise issues. This is one possible solution. Another possibility is a LON to Fiber converter www.Atkinsonelectronics.com LNFR is a great product and easy to use. Where your comm wire is ran under chillers or around th e problem areas you can change to fiber.