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.
If you want to pull the updates from a given section, you need to use javascript and read through the file using the script. AlanG has presented similar scripts multiple times in the forum, so I’m not going to repeat that process. And as far as I know that’s not an automatic process to keep pulling out the updates.
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.