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The problem was caused by the special UI update that accumulates UI events and updates the UI a little later. JavaFX already reused the tree item to an other object and then it was updated to the previous object which was deleted and so showed invalid values. Solution is to not pass the owned object on the asynchronous update object but always read the owned object from the tree item.
the issue is still present for some reason. Has to be investigated.
When a new window is opened then deleted files are not there with fanthom tree items. Also they are not present in the file system. So the problem is the update of the UI tree does not remove objects from the UI tree in some cases.
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