When I add section etc., I run 'C-c C-u C-a' to update all my menus,
but then the menu for the appendix is destroyed.  Try it, and you get:

Before:

  @node Appendices
  @appendix Appendices
  
  @menu
  * Glossary::                    Some of the words used in this document
  * GNU Free Documentation License::  License for copying this document
  * Colophon::                    Version of this document
  * Index::                       Indices of symbols, concepts, etc.
  @end menu


After:

  @node Appendices
+ @menu
+ @end menu
+ 
  @appendix Appendices
  
  @menu
  * Glossary::                    Some of the words used in this document
  * GNU Free Documentation License::  License for copying this document
  * Colophon::                    Version of this document
  * Index::                       Indices of symbols, concepts, etc.
  @end menu

----------------------------------------------------------------------

Another (related?) problem is that the main menu seems wrong to me:

  @menu
  * Appendices::                  
  * Glossary::                    
  * Colophon::                    
  * Index::                       
  @end menu
  
Shouldn't it mention Appendices first and alone, and then the details?
Just like ordinary chapters, i.e.

  @menu
  * Appendices::                  Glossary etc.
  
  @detailmenu
   --- The Detailed Node Listing ---
  * Glossary::                    Some of the words used in this document
  * GNU Free Documentation License::  License for copying this document
  * Colophon::                    Version of this document
  * Index::                       Indices of symbols, concepts, etc.
  @end detailmenu
  @end menu


Thanks!