In an internal plugin I’m building I was using .clone() on an instance node to make multiple instances, but then when I would try to manually change properties on one instance in Figma, all of the other clones would have that property change too.
Further inspection revealed that all of the cloned instances have the same node id.
In the mean time I can work around this by creating new instances of the main component, but I’ll also have to set the overrides I was trying to preserve by cloning an existing instance.