You are talking in very general terms here and no offense, but I don't think you fully understand or know what you want..
Are you talking about encryption while transferring files or while they are saved on your computer and/or server?
If you are talking about transfer, then FlashFXP supported SSL and SSH encryption for many years now.
If you are talking about encrypting files on your disk, then FlashFXP or any other file transfer clients are not appropriate for that task.
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