Does this happen when uploading a file or downloading the file? Are you using Rebex FTP/SSL (Rebex.Net.Ftp.dll's Ftp object) or Rebex SFTP (Rebex.Net.Sftp.dll's Sftp object)?
In binary mode, Rebex SFTP and Rebex FTP/SSL doesn't remove or add any characters at all. This makes it appear that the removal is caused by something else. Have you considered the possibility that it was the previous SFTP software that actually caused the two CR characters to appear?
If you are using Rebex SFTP, try transfering the file using PuTTY's "psftp" command line utility. This is a very simple SFTP client which only supports binary mode and doesn't have any advanced features. Does it behave just like Rebex SFTP in binary mode or not?