AAD Connect v.126.96.36.199 came just a week ago and it had an ugly bug.
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All the user that will be disabled in Exchange Hybrid environments will have their mailboxes deleted from the cloud.
Shared Mailboxes had a long history of misuse inside On-premises Exchange. By licensing rules they have to be disabled users which have a mailbox. So you are not allowed to logon with that account directly but people enabled the accounts and used this way. Not really suitable for a Shared Mailbox.
When we wen’t to the world of Exchange Online, this wasn’t possible anymore as all the users that can logon to their mailbox directly, need a license. And nobody want’s pay more than they could.
If your Exchange Hybrid is made by Microsoft best-practices (Mailflow both ways thru EOP) you will have a problem with Shared, Resource and room Mailboxes in the Hybrid.
Hybrid works with contacts, if the mailbox is in EXO, there will be a contact inside On-premises telling you that your mailbox is in the cloud. If your mailbox in On-premises there will be a contact telling it’s there.
And this is why it will remove all the users having Shared, Resources or a room user inside On-premises AD.
What is synced?
Here are attributes that it will sync to EXO.
And here are the attributes it will write back to On-premises Exchange in Hybrid.
How to fix?
You should be upgrading directly to 188.8.131.52 as the new release isn’t an auto-upgrade.
Release notes history for AAD Connect.
From there you can see the date and high-level notes.
So, please do update if you already have 184.108.40.206 installed or your mailboxes will disappear to outer space.