But what does this have to do with the toilet? As soon as you attempt to re-install the toilet on this newer, higher floor, you may find that there is leakage at the very bottom because the seal isn't tight.
The solution is easy: get a flange extender from your local hardware store. This easy-to-install, inexpensive item ensures a tight seal at the bottom if your new surface will stand half an inch or higher above the existing toilet flange. Simply caulk in with silicone sealer (or rubber gasket, if the package comes with one) and you're done!