thank you for your time and excellent and helpful explanation @Joseph
The document (plain text file) in question is NOT opened by another app but it is cloned to a separate window.
if you are using notepad++ in multi instance with auto backup enabled, it is very important that you don’t open the same document in two notepad++ windows, as they are separate processes and neither one is aware of what has been done at the other window.
instead you should use only one notepad++ window and clone it to the second view:
right click on your document tab, and select clone to other view as seen at the screenshot below.
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now both copies are using the same notepad++ process, and if you start typing, you will see that both, left and right copies, are synchronised without even saving them.
note: if you want to see the unsynced original statically, for comparison purposes, you can copy it’s content to a new document tab on the second view, so that you can have a look at it any time.
it is also recommended that you disable multi instance completely, if you often have to do this.
go to settings > preferences > multi-instance and set it to default (mono-instance) as seen at the screenshot below.
this way a document will always open as a tab at the existing notepad++ process.
Imgur