I dont know about changing from institutional to an individual key, but you can certainly put a script together to remove the institutional key (you'd need the password for a filevault enabled user, I believe). Once thats done, you can have a config profile created and generate a new key and escrow to Jamf Pro.
The command should be fdesetup removerecovery -institutional. My scripting is not that great, or I'd attempt to write something for you
