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I don't know of any way to clear entries off that particular list, but you shouldn't have to go into that list very often.
Your libraries should all be listed on the Library drop-down menu, and if they don't all fit, they should at least be on the Quick Switch submenu. I would think it would be much faster to switch between libraries that way.
In fact, the only reason I can think of to go into that screen is to add a new library to Calibre's Quick Switch, which you should rarely have to do.
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