SkyKick will not delete the backup of the mailbox, and the content will be retained for the duration of the retention period (as indicated in the Settings section of an Office 365 Backup subscription). If the Office 365 license has been removed (thus deleting the mailbox from Office 365), this will pop up an alert titled: Backup [mailbox] not found. To address this alert you will need to disable the backup for the mailbox. For more information about this alert click here. Once the mailbox is disabled, you will no longer be charged for the mailbox and the alert will not pop up again.
In order to maintain the integrity of the mailbox, while removing the need to have it licensed, Microsoft’s best practice is to convert the mailbox to a shared mailbox first, and then remove the license. By doing this, instead of simply removing the license and deleting the mailbox, no mailboxes will need to be created if the customer wants to restore the data. The backups can still be turned off for that mailbox, resulting in no further charges.
Please Note: Disabling the backup of a mailbox will NOT delete the backed up data. Search and restore is available while the subscription is active.