Some things to keep in mind. ANSI is a subset of UTF-8. So if there are no UTF-8 characters then Notepad++ detects it as ANSI. You can force ANSI files to be UTF-8 by using Settings > Preferences > New Document > Encoding and select UTF-8 and apply it to opened files.
Also keep in mind some FTP clients transfer files in ASCII mode which translates the line endings automatically. I’m not sure if NppFTP has an option to change that (I rarely ever use it personally), if not then you probably want to submit a bug/feature directly to that project.