Why did my JIRA Server become unauthenticated with Zendesk after performing a restore/backup?
Performing a backup of your JIRA instance changes the the jira_key associated with your JIRA account. The jira_key is what the Zendesk-JIRA integration looks for and stores in the authentication table in the middleware that establishes the connect between Zendesk and JIRA. Ultimately, a new account id is assigned when performing a backup and it causes deauthorization as Zendesk is no longer certain if it is communicating with the correct JIRA instance. As a result, reauthentication is required.
See How to reintegrate the JIRA integration for instructions are reauthenticating Zendesk with JIRA; no data is lost as a result of this process.