This is a curious question that came across, we are currently using JIRA 6.4 and Jira Agile (Server) and are planning to acquire Service Desk 3.9 Server. can I still use the Jira Licenses from our JIRA instance to be collaborators on the latest version of service desk?
First off, since you're currently using Jira 6.4.x, this means you must be using a Jira Service Desk version such as 2.5.x or earlier. There is a known upgrade requirement for these versions of Service Desk to make sure that they are first upgraded to a Jira 7.0.x and Service Desk 3.0.x version first. This is necessary before you upgrade to any JSD 3.2.x or higher version.
As for your question about licensing, it depends on the name/type/expiration date of license that you have. In Jira 6.x and before these were called Jira Server licenses. But when Jira 7.0 was introduced there were two major changes:
At the time of Jira 7's release there was a push from Atlassian to show more current Jira Server customers the capabilities of Jira Software, so the titles of licenses changed when users renewed to clarify which product you were actually licensing.
In Jira 7, you don't need to license Jira core, provided that you have license either a Jira Software or Jira Service Desk application. The same wasn't true of Jira 6 versions with Agile/Service Desk. Each needed their own license back in those versions.
So a number of users dropped these older Jira Server licenses an instead renewed with a Jira Software license.
So I would recommend going into your https://my.atlassian.com in order to see exactly what license type you have, and when this expires. The expiration date becomes important here because if this is already expired before the date Service Desk 3.9 was released, you can't apply this license to this instance in order to upgrade Jira itself.
But yes, if you have a still current (meaning the expiration date is in the future), you could apply this to the Jira Core in order to add these Jira core users as collaborators in Service Desk. More information on what role these users can have in JSD can be found in Setting up service desk users.
Sorry if I misunderstood your question. No, you cannot use the latest JSD versions (3.9.x) with Jira 6.4.x. You can see from this version history page for Jira Service Desk, that there are specific versions of Jira that must be installed to use any given Jira Service Desk version. As such Service Desk 3.9.1 has to be installed on Jira Server 7.6.1.
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