One way you can do it manually assuming systemctl isn't configured for emacs as suggested previously is to connect to the server instance using emacsclient as you usually do and then close it down:-
I use this:-
(defun server-shutdown ()
"Save buffers, Quit, and Shutdown (kill) server"
(global-set-key (kbd "C-c x") 'server-shutdown)
Note, you can't hope to realistically update a running instance fully and properly without restarting. You are inviting trouble. Re-reading your startup will almost certainly not work for you.
As a side note, I hadn't realised that emacs26 on Debian 10 was indeed configured as a systemctl service - it is. Nice. Note that that call to (kill-emacs) is what the emacs.service "stop" directive actually calls too when invoking the following:-
systemctl --user stop emacs
Note that if you use the code I listed above to (kill-emacs) from a key binding AND emacs is configured and started as a service then it will automatically restart unless you use systemctl to stop it as shown just above.
For those that have an emacs.service in /usr/lib/systemd/user then you can enable this to autostart when you login (on Debian so your mileage may vary):-
systemctl --user enable emacs
And this will install a local use specific service link.