The delete key is the shortcut to delete the current selection of nodes in the workspace - but only if the workspace has focus.
When you open the edit dialog, the focus should shift to the edit dialog - which a quick test here shows it does.
However, I have just discovered that you can use tab to shift focus and get to a point where the workspace has keyboard focus, even though the edit dialog is open. In which case hitting delete will delete the node even though the dialog is open. That's a bug we can fix - even though it takes a few hits of tab to get to the point where you'd notice.
@Surendra Quite why your dialog isn't getting keyboard focus when it opens is hard to say. I can't help notice the
Properties header of your tab has some custom CSS styling going on - is that something you're doing in your environment on purpose?