When I look, I don’t have anything in Edit > File editing > Filetype associations. Since I am at home now, rather than at work, I was able to look at my home FileZilla, which is still able to open files with Notepad++. That said, the simple thing to try is to change your FileZilla association to be php 'C:\Program Files\Notepad++\notepad++.exe' (including the quotes!).
If it’s a problem with FileZilla, then ultimately, a Notepad++ forum is the wrong place to be asking for help, and a FileZilla forum is the right place. If you run Notepad++ normally ( not through FileZilla), does it run? If you Right Click on a file from Windows Explorer ( not through FileZilla), and choose “Open With” and select Notepad++ (or if you have Open With Notepad++ already in your menu, select that instead), does it open Notepad++ with your file? If so, then the problem you are having is not with Notepad++, but actually with FileZilla.
Apparently, my reply didn’t post earlier.