Hi Team, Victor from Jira Align support here

Summary:

I'm from Jira Align support team and we recently evidenced through a high-priority incident that our official documentation doesn't warn the users about the possible impact of using the tool Pull Jira user data + using a custom SSO external ID.

Tech Details:

Customers that use a Custom External ID value on Jira Align > User details from and for SSO login purposes, when I say custom I mean not the External ID automatically provided by Jira integration, can't use the Pull Jira user data area functionality on Jira Align > Administration > Jira Settings > Pull Jira User data > user data pull.
Otherwise, The connector will replace/overwrite every Jira Align user’s SSO custom External ID  with the Jira External ID, used during Jira Align and SSO authentication blocking all the users from accessing Jira Align Platform.

Suggestion:

Since this issue has just happened and was reported in PS-162805
I would like to suggest adding a note of warning on this topic Jira integration setup document > Pull Jira user data area in case you are using this configuration: Custom SSO External ID values in your user profiles DO NOT use Pull Jira user data tool