After upgrading matrix-auth, it warned all specific configurations do not specify user/group entry type. After migrating the entries, all group-based rows display errors “Group not found”.
The groups we used are LDAP-based. I.e. the server uses “LDAP” in the Security Realm setting of the Global Security configuration; the groups refer to the LDAP user groups retrieved dynamically from the LDAP server, not to groups created manually in Jenkins.
The security configuration seems to work even with the error messages.