This is all becoming very complicated… In the Edit Citation-type dialogs, what I have written below is “Traveling library”, as you said. Actually, I think I used to “export to traveling library” command some time ago, since I had lost the file containing the original library. I think this is when all the problems began, because EndNote does not allow you to clearly define what document goes with what library.
I tried fixing all the in-text citations one by one (after unformatting/reformatting), but it is just too much time - plus, since many authors have more than one paper out in the same year, the suggestions that EndNote gives me in the “Select matching reference” windoware not enough so I have to go and find which is the correct reference.
What is strange is that, if I add a new reference to my library, and then use a citation to it in-text, the new reference is added to the list at the end of the document. Therefore the library is not “unlinked” to the document, but - and this is really the problem - the existing references are not updated in the list when I edit them in EndNote. I am at my wit’s end…