What happens when i completley change my internal link structure?

I have a site that i have been working on for a few months in a niche. After i built it and got the main keywords i was targeting on it i read a guide about dragon silos and applied it to the full site. ( my bad ). Most of the keywords i am targeting are showing in the serps apart from 2 that are nowhere to be seen and ironically these are the 2 most valuable keywords i was after. With the metrics of the domain and links iv built to these 2 pages, they should be showing up somewhere in my rank tracker so iv messed up with the internal linking. I wanna just remove all internal links and do them from scratch again. Im guessing when i do this, the keywords that i do have ranking are going to drop?. How long do you guys think it will take after i change all the links for the site to get back to normal?. Would you do anything else like submit the sitemap after changing the links to maybe speed things up. Thanks