PFE will work with Prepar3D ...
... and you DON'T have to install PFE again to work with P3D.
Let's say you already have FS9, FSX and P3D installed on your PC. Provided you have FSUIPC installed for each sim then PFE will work with whichever one is currently running, although for the moment it although thinks you're running FSX when using P3D. However, this isn't a problem for PFE and although I haven't done exhaustive testing It alls seems to be working just fine. Thanks to Pete Dowson and FSUIPC of course.
Here's how to rebuild the PFE database to work with P3D
Using Notepad, create a dummy file named FSX.EXE and save it into the main P3D folder. The content of the file is unimportant but the name is critical.
Now go through the PFE DB Rebuild as normal, but when prompted to select the runways.csv file for FS9/FSX you simply choose the one in your main P3D folder. Provided you have the dummy file (FSX.EXE) named correctly and in the correct folder the rebuild will run. PFE will then create the database files in its \Data folder but they will be named PFE_FSX_xxxx and will obviously overwrite any existing PFE FSX data files you have. So, if you also use FSX you would have to rebuild the PFE database for that sim before using it.
The ideal situation of course would be if you only used FS9 and P3D, then you could use either one without rebuilding the database each time you switched sims.
So that's the current workaround, but I hope to be providing full support for P3D going forward.