I'm having issues with saving files that were modified with "Replace In Files", but weren't already open in Sublime.
-Start Sublime with an empty session
-Do a "Replace In Files" over a directory that has files that will be modified given your find text
What I see then is that Sublime does the replace, and opens the files that were modified. The tabs of the files have the dirty bit dots in their tabs. However, "Save" and "Save As" are disabled in the File menu, and the save hotkeys don't work. This is the case for all tabs open at this point.