I had this issue ... Tech support had no idea how to fix it.
I found this article and they even told me not to do it. As they couldn't give a reason I tried it with a "less important" account.
It was simple, easy and worked.
The steps from support were:
As the users which are having mailboxes both in cloud as well as in on premises was due to assigning the license to those users before syncing it to Exchange on premises and then after syncing the exchange on premises with cloud it resulted in soft match which in turn resulted in two mailboxes. The steps that should be done to avoid it are:
- Remove the license of the users who have two mailboxes (both in cloud and in on prem)
- Then move those users in non sync OU in Active directory
- Then hard delete those users from the cloud
- Then move the users back to syncing OU in Active directory and then run delta sync
- This will remove the mailbox from the cloud
Happy to supply Case number off-line if you want it. The_Exchange_Team