Treat your notes as a project
Emacs has a built-in library for treating a directory tree as a “project”. This means that the contents of this tree are seen as part of the same set, so commands like project-switch-to-buffer (‘C-x p b’ by default) will only consider buffers in the current project (e.g. three notes that are currently being visited).
Normally, a “project” is a directory tree whose root is under version control. For our purposes, all you need is to navigate to the denote-directory (for the shell or via Dired) and use the command-line to run this (requires the ‘git’ executable):
git initFrom Dired, you can type ‘M-!’ which invokes dired-smart-shell-command and then run the git call there.
The project can then be registered by invoking any project-related command inside of it, such as project-find-file (‘C-x p f’).
It is a good idea to keep your notes under version control, as that gives you a history of changes for each file. We shall not delve into the technicalities here, though suffice to note that Emacs’ built-in version control framework or the exceptionally well-crafted ‘magit’ package will get the job done (VC can work with other backends besides Git).