This bug was fixed in the package thunar - 1.0.1-2ubuntu4

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thunar (1.0.1-2ubuntu4) lucid; urgency=low

  * debian/patches:
    - 12_update-cursor-on-delete.patch: properly update the cursor when
      a row is deleted in (Xfce #5361).
    - 13_refilter-tree-hidden-dir.patch: refilter tree model view when
      entering/leaving an hidden directory. lp: #484220
 -- Lionel Le Folgoc <mrpo...@ubuntu.com>   Fri, 15 Jan 2010 22:37:50 +0100

** Changed in: thunar (Ubuntu)
       Status: In Progress => Fix Released

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Thunar doesn't clear hidden directories from sidepane (tree view)
https://bugs.launchpad.net/bugs/484220
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