GitHub for Jira backfill finishes but branches/PRs are missing

[Andrius]

Hi,

I’m a university student working on a software engineering project. Our team has 5 members and we use Jira + GitHub for sprint workflow tracking.

Our GitHub integration was working normally before, but around 4 days ago Jira stopped tracking development activity correctly.

Important setup details:

• We use one GitHub repository
• The integration is connected through my GitHub account
• I am the admin on both GitHub and Jira
• We consistently include Jira issue keys in branch names, PR titles/descriptions, and commit messages
• This exact workflow worked properly before the issue started

What is happening now:

• Branches and pull requests stopped appearing inside Jira issues
• In the Development section, repository activity stopped updating correctly
• I pushed an empty commit to test it, and Jira detected the commit only, but still did not detect the related branch or pull request
• The Create pull request button disappeared from the Development section after the first backfill attempt
• Backfill does not restore the missing development data
• After the reinstallation of GitHub for Atlassian and Atlassian on GitHub, even development data that had previously been synced correctly on older Jira issues became unsynced, and backfill has not restored it. This is a major problem for our team because it affects not only new activity, but also tickets that were already linked correctly before

Important clarification:
The repository is still connected in GitHub configuration in Jira settings:

• it shows under the GitHub configuration screen
• it has Full access
• backfill status shows Finished
• and if I use Create branch, I can still select the repository

So the problem is not that the repository is fully disconnected.
The problem is that the integration seems to be only partially working:

• connection exists
• repo access exists
• commits may still be seen (did not test after reinstallation of the GitHub for Atlassian and Atlassian on GitHub)
• branches and pull requests, however, have not been syncing into Jira issues either before or after the reinstallation for the last 4 days.

What I already tried:

• verified Jira issue keys are in correct format and present everywhere they should be (PR titles, descriptions, branch names, commit messages)
• ran normal backfill and restart backfill
• refreshed after backfill multiple times
• reinstalled/reconnected the GitHub for Jira / GitHub for Atlassian integration
• re-granted all permissions available

What is strange:

• backfill appears to start, but then finishes almost immediately whether or not the “Restart backfill” option is enabled.
• no visible error is shown
• but Jira issues still do not get the missing branch/PR information

Has anyone seen this kind of partial GitHub for Jira sync issue before, where:

• the repo is still connected,
• backfill says finished,
• commits may still be detected,
• but branches and pull requests stop appearing in Jira issues?

Our current sprint ends on April 17, and we started experiencing this issue 4 days ago. So far, nothing has solved it, so we would really appreciate any suggestions on how to fix this.

If helpful, I can attach screenshots of:

• the GitHub configuration page,
• an affected Jira issue,
• and an example PR/branch that contains the correct Jira key but is not being linked.

These screenshots were taken after reinstalling GitHub for Atlassian on Jira and Atlassian on GitHub, and after multiple attempts to continue backfill.

Note: even if the colon is removed from the PR title, as shown in the screenshot, Jira still does not detect the pull request.

[Tomislav Tobijas · Accepted solution]

Hi @Andrius ,

I'll just say that we've noticed a similar issue when it comes to Azure DevOps connection/integration. This started last week and was, potentially, related to a specific global incident that was reported around the same time.

Now, we're mainly testing DevOps integrations, so we didn't have a big impact, but it seems to be a widespread issue for sure. 👀

I've checked with my colleague, and she said that this appears to be fixed (as of today), at least for the Azure part, so the question is - does it seem to work now, or is it still an issue?

Cheers,
Tobi

[Andrius]

Hi @Tomislav Tobijas ,

Apologies for the delayed response, and thank you for checking.

I retested the integration today, and it now appears to be working again. Based on that, it may indeed have been related to the incident you mentioned.

At this point, the integration also seems to be functioning correctly for older tickets, with development information such as branches, commits, and merged pull requests displaying as expected.

Initially, the Development status icon on the Board was not updating correctly for some issues. However, after manually opening the affected tickets and refreshing Jira, the linked branches, pull requests, and commits became visible there as well.

For now, the main synchronization issue appears to be resolved on my side. I will continue to monitor it, but thank you again for confirming that this was not isolated to my team and for pointing me in that direction.