@florent-blanchon ,
Unfortunately, I cannot replicate your problem. If I run v7.7.1, with ComparePlugin added, and put my settings at “Open session in a new instance of NPP” to match yours, and load a few sessions, it opens Notepad++ in the same number of sessions. When I look at Task Manager, I see multiple instances. (So far, this matches yours, and matches expectations.)
But when I exit one of the Notepad++ instances (using Windows X in the upper right or File > Exit), it fully exits that instance, and the number of instances of Notepad++ in Task Manager properly goes down by one. If I have three instances open, and close one, Task Manager shows it drop from 3 to 2; as I close the next two sequentially, Task Manager shows it drop to 1 then to 0.
I cannot replicate your problem discription. I am sorry. Maybe someone else will have an idea of how to help.