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I'm setting up GHAS repos in the Security tab in Jira. I'm able to add most of them but for some reason a couple of repos are not showing up in the GitHub Advanced Security toolchain dropdown. Those repos have GHAS enabled and they are showing up in the Github for Jira toolchain.
As you can see in the screenshot below, fiat-utils repo is added in Github for Jira toolchain but not showing up in GHAS toolchain.
I had a similar problem.
After debugging with Atlassian Support, they suggested that I "Restart the backfill" according to https://support.atlassian.com/jira-cloud-administration/docs/understand-github-for-jiras-initial-backfill-process/
It did take a while to finish. We have 140+ repos, many of which were not available in GitHub for Jira. After it finished, the missing repos are now available to add as a new security container.