If you are syncing with AADConnect to On-prem, you can not manage any of the mailboxes in 365 that have their AD accounts created on-prem, so what you are seeing is expected.
Essentially you would create a remote mailbox and it syncs and gets created in 365 once a license is applied
You would only be able to modify mailboxes in 365 that had both the user account and mailbox created there.
If you were able to modify mailboxes before directly in 365 that were being synced, I cant explain that because thats really not how it works :)