Doing [[note#first#second]] isn’t correct link syntax. If you’ve got multiple headers with the same name, I’m not sure you’ve got a way to specifically target one or the other. It seems it chooses the first one, both when typing manually, and doing auto completion.
If you want to a specific reference you need to add blockId’s to the sections.
For an automatic updated lists of updates related to a project, I would rather use list items tagged with the project somehow, but it seems like you don’t want that solution, so then I don’t know how to do it.