How can I stop the warning that appears in Notepad++ if the file is modified from an external program or application?
Settings -> Preferences -> MISC. tab
In the section that says
File Status Auto Detection make sure that
Enable is unchecked
Settings → Preferences → Misc. → Uncheck Enable under File Status Auto-Detection
Also, as Jet pointed out, you can also have 'Update silently' checked if you want it to auto-update the file.