@Vitalii-Dovgan If you preserve a file’s modified time stamp then Notepad++ does not notice it has changed. Thus it’s possible to sneak in and make changes without triggering the pop-up.
Of course, that also means Notepad++'s in-memory copy of an open file would be out of sync with with what’s on disk. If you do File / Reload from Disk then Notepad++ will pick up the new file contents. Reload from Disk is also available in the right click menu for the file’s tab.