You actually need the free version already installed in order to use the upgrade. So no nothing should be lost when you install the new add-on. Just be sure that the only  MBT plugins you're running are the free version and one of the upgrades. 

So once both of those are installed then you can go and input your license key. Then all the features will be added. If you try to add the license key before you install the add-on or without the free version it won't work.