Set a Controller class to get a list of fx:id.
Select a node (e.g. the root AnchorPane), and set its fx:id by selecting an item in the list.
Type Backspace to remove the fx:id.
Select again another fx:id from the list : the item is not selected, the fx:id is empty.

This is a way to reproduce 100% of the time the selection issue.
But we have sometimes the selection of an item which does not do anything. Playing with the item selection, one can quite easily get the issue.