Am I correct in assuming that the only difference between "windows files" and "unix files" is the linebreak?
We have a system that has been moved
This is only a difference in text files, where UNIX uses a single Line Feed (LF) to signify a new line, Windows uses a Carriage Return/Line Feed (CRLF) and Mac uses just a CR.
Binary files there should be no difference (i.e. a JPEG on a windows machine will be byte for byte the same as the same JPEG on a unix box.)