If I keep the navigational structure (files names) the same, but I completely redesign the website, will the site rank lower for a while because Google does not like to see complete redesigns.
Obviously the redesign would be to enhance the usability and overall appearance of the website. But I do not want to lose ranking.
Google is concerned with the content of your site. The structure of your site may affect ranking if it impedes googlebot’s ability to spider and index your site. The appearance of your site has no effect.
Changing the look of the site while retaining the same structure should not affect things one way or the other.
If you are rewriting the entire content, then you are effectively removing everything in Google’s index and replacing it with different content, so yes, that would take a while for Google to crawl again, and might well affect your ranking, especially in the period before it has all been crawled.
If your changes are primarily to the appearance of the site, rather than the content, then the changes won’t affect the indexing.
I believe I’ve recommended before that you stop obsessing over Google and how Google sees your site, and think instead about how potential visitors see your site. If a thorough overhaul of structure/layout/colour/fonts/whatever will benefit real, human visitors, then just get on with it. Who are you creating this site for - real people or search engine bots?