That's what I see on your 'scope photo. Concentrate on the source of the noise - the VFD cables. You've got far too much RF noise to ever hope to cure it by addressing encoder cables....Something I have discovered recently is that during the install none of the 15 + VFD cables are properly grounded at the motor end. I used Belden 295___ Cables and the installers did not connect the shield at the motor end. I feel like that is likely trashing the entire ground system with PWM harmonics...
Ignore the 60 Hz reading on Fluke. Doesn't mean much. The 'scope is your best friend. Trust it above everything else.