Currently if a Jira project (with associations and bindings) is deleted or archived in Jira, the Association Report will throw the "Failure in running JQL" error (as per screenshot_1).
Once the binding for the orphan (deleted or archived) Jira project is removed from the Bindings (screenshot_2), the Association Report runs as expected.
However if the archived Jira project is to be restored one day, I would like to keep the Bindings in place.
As a solution, allow users to archive bindings (which can be restored later on)
We have created a bug on our backlog for the "Failure in running JQL" error when there is a deleted project in the bindings. You can reach out to our support team to get more information on the bug.