Project Professional 2013 is not compatible with the Office 2016 version of Office 365 ProPlus. Microsoft recently announced availability of the Office 2016 version of Office 365 ProPlus.: https://technet.microsoft.com/library/mt422981.aspx
One of the details caught our attention:
You can’t have a volume licensed version of Visio 2013/2016, Project 2013/2016 or Project Professional 2013/2016 installed on the same computer as the Office 2016 version of Office 365 ProPlus.
This will be an issue if your organization is currently using the volume licensed (non Office 365) version of Project Professional 2013, along with the Office 2013 version of Office 365 ProPlus. In this case when Office 365 ProPlus is upgraded to the 2016 version, Project Professional 2013 will be uninstalled and you won’t be able to reinstall.
In summary, as of this writing you cannot use a volume licensed (non Office 365) version of Project Professional with the Office 2016 version of Office 365 ProPlus.
If your organization is upgrading to the Office 2016 version of Office 365 ProPlus you must use either the 2013 or 2016 version of Project Professional for Office 365 (non volume licensed).
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