Ah I see. So the user has two Atlassian accounts? If so then you could simply find all issues where the user exists (assignee, watcher, reporter, custom user picker fields) and go thru and bulk edit these fields changing to the user account that is to remain. Also, look for where that user might be a project admin, component lead, etc. Messy process and maybe there is a better way via some addon to migrate user but unfamiliar with this. Once complete deactivate the unneeded user.
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