When I was using WS-FTP it had a feature to add the "l" to htm during uploads and delete it during downloads so the file names are easier to read and don't have the ~'s added to them.
I haven't found that feature in your program or maybe it isn't there?
Why do you bother about this now, 8 years after long file names were introduced??
Also the downloads become all caps which contributes to the difficulty reading file names in my html editor. The other program also had an option of forcing lower case transfers.
Please read documentation