If you changed the primary author or the year, it is likely that endnote doesn’t know that the updated record matches the citation so it is pulling it from the “travelling library”, but I don’t know why unformatting to temporary citations wouldn’t prompt you to select the new corrected record in matching?
Best way to correct a record in the library already used in a paper, is to do so from the citation, right click edit citation, more, and then find the citation and select the “edit reference” > edit library reference – correct it there, and going back should update the citation and retain the link.