When restoring a Mail or OneDrive folder to a previous version, will the restore overwrite the latest version?

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Definitely NOT.

Safe restore

By default, all restored data will be placed into a separate folder named Restored <date-time>, in order to distinguish it from the original data. If you choose to restore the data to a specific folder (even the original folder!), CubeBackup will not overwrite any files in that location. The restored data will add a prefix of timestamp to the name.

More information about the data restore is available at How can I restore my backups to a specific folder?.