This is an issue that is starting to come up as web developers are makign dyanamic mobile sites with multiple navigation options. Create more navigations will essentially create different sites, so the confusion is entirely understandable. A website may be designed with differ navigation headers, which may affect the way that Google's bot crawls your website.
Check Your Links For Consistency
In theory, if your links on each page's navigation are exactly the same, it should not affect the way Google ranks your website. The Google crawler will be able to examine both navigation menus and discern that it is just a separate navigation option. What you should focus on when designing navigation links is the way it affects the users' interactions and if it makes them leave the page.
Should You Use A Separate Navigation View For Mobile Users?
If the mobile version of the navigation menu does not take away from the overall experience of the website, then you should definitely make a mobile-friendly menu. Since mobile phones have such cramped screens, it is a good idea to make a reactive interface that will make a simplified menu that is easy to use with a touchscreen. On the other hand, many mobile users may be turned off by the fact that you are limiting their options available on the screen, so make sure to still give mobile users a freedom of choice with their menu usage.
Important Pages Should Go First
Ditch the idea that your menu should be in alphabetical order. In order to optimize your SEO to the most important parts of your website, your navigation menu should display the most critical links. Google will crawl these first and it will give you a slight advantage of displaying your website in the proper way. When it comes to mobile navigation, it would be convenient to display the most important links so that mobile users may easily click on them.
Short and Sweet For Mobile Users
Mobile users have a limited amount of space and data, so cut things short and let them browse with ease. Disable unnecessary graphics that may clog the screen and create shorter page descriptions.