We don't know what you had configured, how you did the upgrade, or, most importantly, what you've set up to do this "Salesforce Desk.com links". I suspect they were being done by an add-on of some sort, and that add-on needs an upgrade to handle the version of JIRA you have gone to.
Also, I don't know what links from Desk.com to JIRA you have configured. It may be that they were set up for SOAP access, which JIRA dropped in 6.4. You'd need to replace them with REST. But it could well be something else handling those links.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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