By default, Word places endnotes on the same page as the last text in the document. If you want them on a separate page, you have to add a manual page break (Ctrl+Enter) at the end of your document, before the endnotes.
This may happen if both the page footer and the footnote text exceed five lines and a section break appears on the same page. If you can't remove the section break, add some blank lines above the footnote text in the Footnote pane.
You may have deleted the footnote text in the Footnote pane, but you also must select and delete the footnote reference mark in the document.
Check: Did you format it with one of Word's built-in heading styles (for example, Heading 1 through Heading 9)? If not, do so. If you can't (or don't want to), select it as a bookmark and cross-reference it the same way you would cross-reference any other bookmark.
Make sure that the subdocuments your cross-references refer to haven't been removed from the document. Make sure that they are available and open.
For more information about working with master documents, see Chapter 19, "Master Documents: Control and Share Even the Largest Documents," p. 653.