Sorry for the long delay in reply.
\appdata\roaming\notepad++\plugins\NppFTP.xml
Was that a typo for
...\appdata\roaming\notepad++\plugins\config\NppFTP\NppFTP.xmlor did you really expect the NppFTP.xml file to be at the top level of the plugins folder?
But that said, I doubt that’s your real problem. I don’t know anything in the installer/upgrade process for the Notepad++ app itself that would wipe out your previous plugins config – I’ve never seen that happen.
Unfortunately, if it has happened, there’s not much we can do to recover it. Recuva or other file-recovery software might help, but we’re not experts on such software here. (But if you only had a few, it’s probably easier just to rebuild the list inside NppFTP.)