You will have to first confirm if the object is in deleted container in Azure AD portal. You can confirm this by selecting Uses >> deleted users in Azure AD.
If you find the user in deleted container, then you can check the deleted date time. Once you have the date and time you can check the Azure AD audit log to confirm who has deleted this user.
In audit logs, if you see AD connect connector account as actor then it is proved that AD connect deleted this account.
Now, to check why AD connect deleted this account you will have to troubleshoot this from AD connect side.
You can first confirm if the OU to which user is part of, is in sync scope of AD connect. Post that you can search the user in metaverse search to start with.
You can use below article to troubleshoot this further,
Let me know if you have any further questions regarding this
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