Saving will only be allowed, when all conflicts were solved. If the file already exists and the "Backup files"-option is enabled then the existing file will be renamed with an ".orig"-extension, but if such a file exists it will be deleted. When you exit or start another diff-analysis and data wasn't saved yet, then KDiff3 will ask if you want to save, cancel or proceed without saving. (KDiff3 does not catch any signals. So if you "kill" KDiff3 then your data will be lost.)
Line endings are saved according to the normal method on the underlying operating system. For Unices each line ends with an linefeed-character "\n", while for Win32-based systems each line ends with a carriage-return + a linefeed "\r\n". KDiff3 does not preserve the line-endings of the input files, which also means that you shouldn't use KDiff3 with binary files.