SourceTree will convert a whole file from CR-LF (win) to LF (linux) if you use the "Discard Selected Lines" function for a CR-LF file on Windows.

Reproduce:

• Under Windows, create an ANSI file with CR-LF ending and check it into your repository.
• Modify a single line (or multiple lines) inside an external editor (notepad++).
• Select some lines of this file inside SourceTree and chose "Discard selected Lines"

Result:

• The whole file will be converted to LF and for this marked as 100% modified.