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It sounds simply like you have calibre showing you a subset of your library. There are several ways to have that happen:
1) Simply clear the search to go back
2) Uninstall the View manager plugin, you've probably got it configured to show a virtual library at startup that only has a few entries in it
3) Make sure you dont have the setting in Prefrences->Behvaior->Virtual library to show on startup enabled
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