What backups were you running?
By default, the atlassian stuff runs regular simple xml backups regularly, so if you just installed and ran with them, they probably have backups you can import into a new clean system (server or cloud). For Jira and Confluence, the backups will be zip files under the export/backup directories in the home directory for them, plus you'll need a copy of the attachments directory, also in home. For bitbucket, you'll also need to think about the git repositories.
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