It seems I'm having some issues with the binary transfer setting not working.
We recently upgraded to a new server with Ubuntu as the OS which had java 7 installed. We were previously running edtftpj pro 4.2.0 on an older java 5 Debian server without any issue, but 4.2.0 seemed to have some issues on the new machine so I put in 4.6.1. That fixed the issues I was seeing, but we started noticing that all files transferred using SFTP which had CRLF at the end of line were converting to LF. If I understand correctly, binary mode should transfer files exactly while ascii mode would do the EOL conversions.
The code itself hasn't changed and is still setting
client.setType(FTPTransferType.BINARY);
after connecting.