You can override the existing installation tree but you still need to restart your running Nginx server from the new executable. Usually we do something like this:
You can also just stop your current Nginx server and start it from scratch again if you don't care about the down time in between.
But please note that HUP reload won't update the running Nginx server processes with the newly installed executable file.
If you are using shared memory storage in your Nginx server (like Lua Nginx Module's shared memory dictionaries), then a full server restart will clear all the data in the shared memory zones. So be careful here.