Try the following in powershell to see whether your CSS file is customized: .........
$web = get-spweb http://yourweb
$f = $web.GetFolder("Style Library/folder/css")
$f.Files |? {$_.CustomizedPageStatus.ToString() -eq "Customized"} |% {$_.Name}
If it's customized, use the following to revert back to unghosted mode:
$f.RevertContentStream()
Reference here.