How to backup InnoKB databases?
InnoKB stores all databases under the default ‘[install-dir]/repository’ folder or your custom repository directory. To backup a database, periodically archive the database folder including all files by using a zip/tar utility (e.g. WinZip, WinRar or Unix tar). Note that before making backups for InnoKB databases, please be sure to first stop or pause InnoKB service, in case of any file access conflicts. To backup the server configurations, just create backups for both the ‘innokb_config.xml’ and ‘innokb_grant.xml’ files.