I think we have figured this out.
In addition to placing the filter on LDAP so that Jira/Stash only see the one true user with the email address being used in Git, we needed to break and recreate the Application Links between Jira and Stash and then resync the user directories.
In addition to directory caching it seems that their may be caching of interactions between the servers as they interact via the application links.
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