Problem

Jira linked with DVCS integration to Github Enterprise Server does not synchronize Pull requests after setting up a new Github instance

Diagnosis

Soft sync scheduled sync job does not retrieve anymore any newly pull requests pushed and linked to issues.

Cause #1

A bug has been introduced in Github Enterprise version 2.22.0, 2.22.1 or 2.22.2 so that on a freshly set up 2.22.0, 2.22.1 or 2.22.2 instance or after upgrading to 2.22.0, 2.22.1 or 2.22.2, the activity feed on an organization's dashboard would not update.

Since soft sync does retrieve the pull requests info from the activity feed, no update is consequently found and ported in Jira.

Cause #2

GHE has rate limiting configured and it's blocking Jira's requests, you'll have the following messages appearing in atlassian-jira.log:

"2021-12-02 23:18:22.162","com.atlassian.jira.plugins.dvcs.exception.SourceControlException: Could not retrieve list of branches
	at com.atlassian.jira.plugins.dvcs.spi.github.GithubCommunicator.getBranches(GithubCommunicator.java:539)
[...]
Caused by: org.eclipse.egit.github.core.client.RequestException: API rate limit exceeded for user ID XXXXX. (403)

Workaround #1

Forcing a full sync while holding SHIFT and clicking on sync on one of the affected repo in the DVCS account page is a valid workaround to retrieve the pull requests anyway.

This will completely remove the existing data from Jira and perform a complete sync of the repository. This can be a very timely and expensive operation.

Resolution #1

Upgrade Github Enterprise Server to at least version 2.22.3 as per Github Enterprise 2.22.3 release notes to get this fixed.

Resolution #2

Increase the  GHE rate limit settings and verify if the error message still appears, adjust value accordingly to demand.