You are still speaking in generic terms regarding your specific use case.
Are you using that remote server simply as an offsite backup solution? What kind of files are you uploading? Does a remote server need to work with those files?
From what you said so far it sounds like you should be encrypting your files locally on your computer before uploading them to that remote server. For that there is a huge myriad of tools, most popular being PGP-related ones and truecrypt.
In order for FlashFXP to support anything, FTP servers would need to support that kind of encryption as well and afaik there's no such standard.
Also, no matter what algorithm you use, scrambling file/dir names is silly. That is
security through obscurity and it doesn't work. You should worry about securing the content of your files, not hiding them with different names.