You are editing the file in Notepad++ while it is also open in the debugger editor, and then you debug it? That workflow is definitely not supported in the debugger. It will cause multiple problems, including trashing your bookmarks, breakpoints, and watch list, which are loaded when the file loads in the debugger, not when / if the debugger detects that someone else has modified the file.
Breakpoints (and bookmarks) are saved as annotations in the file by the debugger editor. There is no provision for this if you're using an external editor. If you are determined to use Notepad++ as your editor (not sure why, because Notepad++ and the debugger editor use the same Scintilla internal editor) you should not start the debugger until you have finished your edits, and then close the debugger before you make any new changes in Notepad++.