I have buttons and a lot of inter-button connections.
(Sorry I goofed with the screen shots.)
First one you can see the nodes with the links.
I delete the one indicated. (Cropped picture)
When deleted, the nodes show as changed but the deploy is not active. (Bigger picture)
I am actually running several instances of Node-RED on my server, each implementing different parts of my system, including instances for testing new flows or features.
That comes in very handy during upgrades, because I am able to upgrade them separately to a new version. E.g., I kept one instance still running 0.20.8, while all others run on 1.0.1 now.