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Start Sigil, open Edit->Preferences, click on the Open Preference Location on the bottom left to open the directory containing the preferences files in your file browser.
You should see a sigil.ini file there (if not, then that's pretty odd since it will get created automatically if it doesn't exist, at least if you exit at least once if not before).
If your clips and saved searches are still around, they should be in that file. You can copy the file or remember the location, and in Saved Searches do a right-click and select Import, then select that file from the file browser that opens. If there is any data it should read it in.
I don't know if your update process uninstalled or deleted the old configuration files or overwrote them - but if they did, then it looks like they are gone.
However, I've installed that ppa fine and uninstalled it okay and it left my old configuration file as is in both cases on Ubuntu 12.04.
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