One way that I've found that works is to manually download the entire remote directory to the local temp directory using, for example, WinSCP.
After downloading all the files, NppFTP works exactly as if I had selected the file and opened it in its interface, and uploads it when I save the file in Notepad++. It searches the contents, and if I click a result in the "Find results" dialog, it opens the file to that line.