Calibre does not maintain a separate list of tags. The list is basically the sum of what is on all books. If only one book has a particular tag and you removed that tag from the book, or deleted the book, calibre will completely forget the tag.
The only workaround I have seen for this is to create a dummy book and add all the tags you ever want to it. That way they won't disappear when you edit a book and will appear in the lists to select from.
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