The Windows XP version should work. I don't do Windows 7 so I can't tell for sure.
Create a working folder and download the flip program into the new folder. Copy a few files from you site into this directory for testing.
Go to the command prompt (dos) and type this command (assuming you have a file called test.php):
flip -t test.php
This will tell you what the current file type is.
To change it to Unix type:
flip - u test.php
To change it to DOS type:
flip - d test.php
Unfortunately it does not understand wild cards, so you will have to repeat for each file. Use the up arrow to bring back the last command entered and backspace over the last file name and use the tab key to cycle through file names.
If you have a lot of files you might want to do them in batches, moving the finished ones to a different folder, and copying news ones in for processing.