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Hi SamuraiS,
It's OK to delete the migration batch if you have confirmed the following key points:
- You have already pointed the MX record to Office 365.
- Users are using the Office 365 mailboxes and can receive emails directly in Office 365.
- All emails that were sent to the on-premises mailboxes before the MX record is changed have been synced to the Office 365 mailboxes.
Deleting the migration batch won't remove the current mailboxes and emails in Office 365. Depending on the number of the users, it may take some time for the batch to be deleted. It's an expected behavior and won't affect the Office 365 services.
Thanks,
Henry