You can delete a mailbox from an Exchange Online app.
If you added the Active Directory group to the Exchange Online app, and the mailbox is included in the Active Directory group, then the mailbox will be added back to the app when the next backup runs.
Procedure
From the navigation pane, go to Protect > Office 365.
The Office 365 apps page appears.
In the Name column, click the app that contains the mailbox.
The app page appears.
You can delete a mailbox based upon the following requirements:
To exclude a mailbox from further backup operations, in the row for the mailbox, click the action button
, and then click Manage > Remove from content. The status of these mailboxes is updated as Deleted.To permanently delete all the data that has been backed up, in the row for the mailbox, click the action button
, and then click Manage > Delete from backup. The data is no longer available for browsing and recovery. A confirmation dialog box appears.
Click Yes.
Tip: To see deleted mailboxes, on the Mailboxes tab, click the gear button
, and then select Clear all filters. In the table heading row, click any Column Settings button 
, and then select Columns > Status. The Status column is added to the table. To delete mailbox items, folders or messages, on the Mailboxes tab, in the row for the mailbox that contains the item that you want to delete, click Restore, and then click Restore messages.
The mailbox contents appear.
To delete a mailbox, do the following:
In the left pane, select the checkbox for the mailbox,
Click the action
button, select Delete.
To delete a folder or a sub-folder, do the following:
In the left pane, expand the mailbox, and then click the folder or the sub-folder.
Click the action
button, select Delete.
To delete messages, do the following:
Either expand folders to navigate to the messages in the right pane, or in the Search box, enter search terms in the search filter list.
For example, enter inbox for the Folder filter.
Select the check boxes for the messages.
Click Delete.