You should only use the remove option with nodes that are flagged “unknown” and you are sure the device isn’t present or associated anymore.
Never do it on an active node, that will force you to have to re-add that device to Homey (and probably first reset the device because that thinks it’s still associated with Homey).
Sometimes the remove option is grayed out with an “unknown” node. Then first click on “heal” and after it says healing isn’t possible the “remove” option should be enabled.
To answer your question: as far as i know you have to do it for every unknown node.
