the icon on the left is revert
the icon on the right is clean
when you save a node to tscn file(it like prefab in unity).when you add the tscn to other node,
the left icon is revert status to the tscn's status,
the right icon is clean status to empty
like this

One more thing, you cannot make it empty by selecting an empty node, you can only make it empty by the right icon,This should be the root cause of the design