I am not sure that there is any problem to spend time resolving. It seems, but I am no expert on the innards of Calibre, however, as others have said that this is a history list. It is also a list that is not ordinarily used in the day to day use of Calibre - it presents a list of possibilities from the past should one ever have necessary recourse to that part of the menu tree.
If so, perhaps it should be looked at it in the same light as one would with the recent documents lists in the likes of the Microsoft Office applications, etc., for example, where those normal and low levels of anxiety do not get their knickers in a twist if there are items on those history lists which no longer exist, or which have been later moved to another folder and so also made inaccessible from the list. One can, of course, often (but not always) clean those lists by setting the list length temporarily to zero, or for which tools such as CCleaner will also clear for popular applications; but whoever bothers much?
Unless there is some other special importance of the list being correct for Calibre to operate correctly and be used efficiently, which is doubtful, it looks to me that people may be looking for a problem here when there really is none
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For the record, there are 10 libraries in my own list, some of which still exist and others that do not. I am quite confident that I have over the course of time created more libraries that that (and which been deleted) and so it may be that the history list is a stack 10 deep, last on top - well 10 is a nice round number anyway
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