[KevinH]

Historically, the ncx page list is simply not used for epub2 so Adobe created its page-map.xml file. Page lists are part of the spec for NCX but nothing ever seemed to support it. Same for ncx landmarks. The opf guide is used instead. Really the only thing the ncx is typically good for is the toc.

Under epub3 the nav page list should be updated for every move and rename of files, but I am not sure about deletes. I will try to recreate what you are seeing. If so it is probably a bug but one that has existed for a long time, as nav page-lists are quite rare.

Manually rebuilding the nav page-list after deletes is probably a good idea as you may want to assign that page number to some other file otherwise you will have to manually rebuild all of the page number labels!