A shard mailbox (ghost) was detected for "User Email". No synced mailbox available in the mail store for this user. This may cause undesired migration results.
This error refers to mailboxes in O365 being created as Shard mailboxes (not to be confused with "Shared" mailboxes). These are essentially a ghost or placeholder mailbox created to hold information for a user that does not yet have a mailbox in which to store data.
To determine if a mailbox is a Shard mailbox, use PowerShell to connect to your Office 365 tenant and run the following command:
Get-MailboxLocation "EMAIL ADDRESS"
Note: Replace "EMAIL ADDRESS" in the command with the email address of the mailbox to be checked.
Example of a SHARD mailbox:
MailboxLocationType : ComponentShared
How it should be:
MailboxLocationType : Primary
Shard mailboxes are often created when using AADConnect without setting the msExchMailboxGuid to null and then licensing the mailboxes in Office 365. When looking at the user mailbox in the Office Admin portal, you may also see the message "This user's on-premises mailbox hasn't been migrated to Exchange Online. The Exchange Online mailbox will be available after migration is completed." These mailboxes are not able to be logged into through OWA. See How do I test mailbox access? for instructions on logging into a mailbox through OWA.
Per Microsoft, any data migrated to a Shard mailbox is retained and once a primary mailbox is created for the user, the Shard mailbox and the primary mailbox will be merged.
Once the Shard mailboxes are identified, set the msExchMailboxGuid to null and re-sync with AADConnect. For more instruction see How can I set msExchMailboxGUID attribute to null? If this does not resolve the issue, the affected mailboxes should be deleted from the Office 365 tenant and imported back into the Office 365 tenant either via CSV or AADConnect with the msExchMailboxGUID attribute set to null.