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It sounds like as part of the Atlassian account move I need to "Verify My Domain"?
What exactly am I verifying and why? Am I just verifying that I own the email domain?
I use two different email domains to log in so If I verify one will it impact my ability to log in with the other?
This whole process was not explained well and the fact that I cant talk to anyone at Atlassian makes it worse.
For some background as to why this is happening please see The Upgrade to Atlassian Account.
If we haven’t upgraded your users yet and you have a password policy, you must verify your domain to keep your policy.
I would recommend taking a look at that referenced Atlassian blog post: Domain verification
From that page:
Domain verification allows your organization to centrally manage all its employees' Atlassian accounts and apply authentication policies.
Basically, all of the user accounts in Cloud are being changed over to this new system, and in order for you to be able to manage all the accounts with your domain(s) Atlassian needs to verify that you actually are the administrator of that domain.
Using different domains for user accounts in your Cloud instance is still be permitted, however if you are the admin of this cloud instance, you might not be able to enforce a password policy for all the accounts in that cloud instance if they original from domains you do not control.