We have a new company domain name (internet domain not the MS one). We use LDAP user directory for JIRA and Confluence. Our users log-in fine but when they send email their "from email" field is the new one and the incoming mail handler does not recognize them as users. I observe the user directory through JIRA and see that all users are represented by their old domain name (i.e. user1@oldDomainName.com).
I have one user in local directory with a user@steadySameOldDomainName.com that is well handled by the incoming mail handler.
I'd imagine you need to ensure the LDAP is updated with the new addresses and then run a full synchronization. Administration -> User Management -> User Directories.
If you have users in the local directory you can update the using the API. Bob Swifts JCLI is my tool of choice for this sort of thing: https://marketplace.atlassian.com/plugins/org.swift.jira.cli
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