We were coming off of a full reindex of Jira datacenter.
When I use the "updated" field in the jql it only finds the issue when I do a manual search via "Run Now" (preview), and it shows in the log and does the subsequent transition.
But when I let it run automatically via cron expression, then it doesn't find the updated issue.
I have a feeling that something might be cached or some user context is missing when the job runs by itself or maybe you just can't use "updated" in a ScriptRunner job JQL query or this is exclusively a datacenter problem?
The job should have a "run as" user configuration.
Try to "impersonate" that user and run the JQL to see if you get results.
It's possible that in the "run now" scenario, the JQL is executed with the current user's permissions and you can see those issues. But your run-as user might not have that permission.
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