The standard jrk firmware has no limit on how fast the motor can decelerate. Unfortunately, there is not enough room left on the jrk to include this feature without losing others. If this feature is important to your application, you can find custom versions of the firmware with deceleration support in this forum thread. There are two files in that thread; please take note of whether you have a jrk 21v3 or jrk 12v12, and download the correct firmware for that version. Additionally, please note that the max duty cycle limit and current limit features were removed from this version of the firmware to make room for the deceleration support.
As noted in that thread, after loading the correct settings file onto your jrk using the Jrk Configuration Utility, you can set deceleration limits in the Motor tab using the boxes labeled “Max. duty cycle”.