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Yes, if a customer already has an Atlassian account, when migrating their account it will just make them an internal user and also, for them to be able to access their tickets that they opened when they were customers.
If they have both a customer and an internal account on your site, the migration will merge the accounts. The customer account will be set as inactive and all the tickets created by them, comments, and any other history will be migrated to the internal account.
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