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
If you are just interested in the content of text files, then yes the line endings are different. Take a look at something like dos2unix, it may be of help here.
(Of course there are many other things that make unix and windows files different, but I don't think you're interested in those other differences right now.)