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:

After the user Data pull  button a  confirmation dialog box should appear and explain the user what this execution exactly does with the user fields and alerts about potential impacts