WARNING: The NavigationMenu. Error update from 3.1.0.1 to 3.1.1-4

Hello, I am trying to update from 3.1.0.1 to 3.1.1-4, when I update the database with the command
(php upgrade.php upgrade) by console I receive the following alert:

WARNING: The NavigationMenu (ContextId: 2, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 2, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 1, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 1, Title: Primary Navigation Menu, Area: primary) will be skipped because the specified area has already a NavigationMenu attached.
WARNING: The NavigationMenu (ContextId: 0, Title: User Navigation Menu, Area: user) will be skipped because the specified area has already a NavigationMenu attached.

After the update I detect that not all the shipments appear, some are missing.
I have read in the forum a similar problem with the following solution before updating but it has not worked.

ALTER TABLE books_for_review_settings CHANGE COLUMN locale locale varchar (14) NOT NULL DEFAULT ‘’;

then try to make that change in the following tables
books_for_review_settings
group_settings
referral_settings
review_object_metadata_settings
review_object_type_settings
static_page_settings

I appreciate any suggestion
Thank you