There is a way to encrypt (and decrypt) existing files via the SSH command-line. See the encrypt command in the command list here.
If you obtain a file listing of files to encrypt, you could generate a script to be run to encrypt each file as described here. Your script would consist of a series of commands like this:
encrypt -s /home/myuser/test_plain.txt -d /home/myuser/test_encrypted.txt
Note that it uses paths from the virtual file system, not Windows.
We recommend trying out a single file to start with and check that it is working as expected before you encrypt the entire file system. And consider backing up your files first!