EncFS ( Porta do Windows ) pode fazer isso com sua opção --reverse
:
Da página do manual:
--reverse
Normally EncFS provides a plaintext view of data on demand. Normally it stores enciphered data and displays plaintext data. With --reverse it takes as source plaintext data and produces enciphered data on-demand. This can be useful for creating remote encrypted backups, where you do not wish to keep the local files unencrypted.