Will backup data persist when files/emails or even users have been deleted from my Google Workspace domain?

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Absolutely.

Files and emails are restorable

CubeBackup is a backup service, not a synchronizing tool. All backups, whether Google Drive files or folders, Gmail messages, Google Contacts, Google Calendar events, or even entire user accounts, are permanently saved in the backup files and not affected by future changes you may make online. These files can be restored to any state in their version history at any time.

Deleted accounts

Even when a user is removed from your Google Workspace domain, CubeBackup will still keep all data for that account as part of your backup. The data for the removed user can easily be exported, or be restored to another active user.