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Subject basically describes the problem: this morning I am logging into my Xubuntu 16.04 machine as I always do, but the whisker menu lost all my customizations: sizes and especially favourites! It is reset to the list of favourites of a fresh install. Otherwise the system seems to be unchanged. Why does this happen, and can I prevent it? Can I somehow retrieve my old list of favourites somewhere?
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As for the why, you'll have to review your log files. The specific ones to look at would be ~/.xsession-errors and ~/.xsession-errors.old (assuming that something was logged). Note that if you have logged in and out since then, the log files will be overwritten and you may have lost any relevant information.
Regarding the retrieval of old data, the whskermenu stores it's configuration information in ~/.config/xfce4/panel. What is the contents of that directory? Perhaps there is an old saved file in there that you could use.
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