Hi,
in special circumstances blocks can vanish completely.
Check the following procedure:

1. You need the block "Navigation" configured with the following options:
   1. Original block location: System
   2. Page contexts: Display throughout the entire site
2. Click on "Turn editing on".
3. Go to "Navigation / My profile / Messages.
4. Click on "Configure Navigation block".
5. Go to the setting "Display on page types" and set it to "Any message pages".
6. Save this configuration.
7. The navigation block is vanished!!!
   You can not find it in the "Add a block" list or anywhere else.
   The only two way I found to get the block back is:
   a) Change the pagetypepattern to "*" in the table "block_instances" inside the database.
   b) Remove this block in the blocks configuration and add it again.
   Best regards
   Andreas