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Currently when FXD file is invalid whole navigator tree disappears. It should however still show the as much as possible of the file structure and show error(s) in the respective nodes using error badges & red color.
It depends on http://javafx-jira.kenai.com/browse/RT-1965
Closing all bugs filed against JavaFX 1.x as wontfix. We will support JavaFX 2.0 - please keep opened only bugs against the new release. Thanks.