Stop Notepad++ warning if file has been modified from outside

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.

Uncheck 'Enable' to disable update detection or check both 'Enable' and 'Update silently' to automatically update once a change is made.

Settings -> Preferences -> MISC. tab

In the section that says File Status Auto Detection make sure that Enable is unchecked

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