If anything is to blame, it is LyX. Whether there is a bug in LyX or not
depends on the folder you backed up. Can you send me the folder that you
backed up to skost...@lyx.org ? Can you please check and let me know if
anything is personal and you wish was kept private?

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https://bugs.launchpad.net/bugs/1430059

Title:
  Many options in various menus appear greyed out, inaccessible

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