1. Your program should contain some default settings if the settings file isn't found. You could pop-up a dialog box asking the user to confirm some settings, but you should hard-code some defaults if you can't find the file.
2. There is no method of file protection that Windows Explorer can't undo. By default, Explorer doesn't display hidden or system files, but users can change these options. Depending on your Windows security settings, you could put the file in a directory that only an administrator has read/write access to, but then regular users wouldn't be able to update it.
3. You may be better to store the settings in the Windows Registry rather than in a file. Then you won't have to worry about the file being deleted. See the sample that ships with CVI: ..\CVI\samples\apps\regadd. The Programmer's Toolbox has Windows Registry functions. Add ..\\CVI\toolslib\toolbox\toolbox.fp to your project, then on the project window menu, goto Instrument >> Programmer's Toolbox >> Windows Registry (with Flatten not checked) to see the registry functions. Again, you need some defaults if the registry keys aren't found.