Please follow the upgrade instructions in the GreenHopper Installation and Upgrade Guide, plus note the following:
GreenHopper 5.9.1 is only compatible with .x.
In addition to the above, please read the GreenHopper 5.8 Upgrade Notes and the Upgrade Notes for every version you are skipping during the upgrade. The complete list of Upgrade Guides is available here.
Please re-index and re-start JIRA after ugrading to GreenHopper 5.9.1 from GreenHopper 5.7.x or earlier.