Written by Thomas Speekenbrink
Customers running the Exchange Online Synchronizer version and who will convert from Exchange On-Premise to Office 365 will get duplicates as soon as the Synchronizer will be linked to the Office 365 environment.
Why does this happen?
After the conversion to Office 365, the userstore_id's will be changed and the users cannot be matched anymore. You will have to re-link the users. This will delete all Synchronization history and thus create duplicates.
Unfortunately we cannot offer a conversion tool for this, because we can't predict the new userstore id's in a Office 365 environment.
To avoid duplicates the Outlook Calendar, contacts and tasks need to be cleaned.
See this article on how to do this: Clean the Outlook calendar