see:See: http://blogs.technet.com/b/projectsu...i-upgrade.aspx
Specifically:
Now you know it is safe to upgrade – and also what features you can expect I will tell you about a couple of things of which you need to be aware.
1. You cannot mix versions if you are running click to run installations – so upgrading an Office ProPlus click to run install from 2013 to 2016 will want to uninstall and 2013 click to run products it finds – such as Project and Visio for example. You will need to update to the 2016 for these too.
2. You cannot mix click to run with msi based installers of the same version. This means you cannot run Microsoft Office 365 ProPlus (which is click to run) with an MSI based installation of Project Professional 2016. You could either change to Project Pro for Office 365, or get a click to run Project Professional 2016.
3. You can mix different versions and different install technologies – so running Project Professional 2013 (msi installation) is fine with Microsoft Office 365 ProPlus (‘16’ level – click to run)