Parker 590 encoder

If you were willing to spend all day tuning the machine, you might be able to get the sound to go away.  But that would defeat the purpose of having an encoder because you would need to set your gains so low they would not hold speed accurately.  My recommendation would be to locate the damaged component and replace it.  That would be one of the following:

• The encoder.
• The encoder cable.
• The encoder card on the drive.

Technically, any one of these components could be damaged.  However, I think the encoder is the most likely component to have failed.  Encoders are often in harsh, vibrating environments.  In addition to electrical failures, they can have bearing failures and suffer contaminant ingress, which makes them read incorrect speeds.

The symptom you describe does not sound like a total encoder failure but a partial one, leading me to believe the encoder itself is the problem.  I would replace the encoder at the earliest possibility, even if you have to get one with a different resolution.  If you need to get one with a different voltage, the AH387775U001 encoder card can be calibrated for 5, 10, 15 or 24 VDC.

https://www.parker.com/Literature/SSD%20Drives/DC%20Drives/HA470388U003.pdf#page=125