I'm not familiar with the particular errors you are getting, but one thing you could try is to double click the error and the modeler will take you to the page that is causing the error. From there you can change the layout of the page that to something that's in your Navigation Layouts module.
Hopefully this helps. If not, can you show some screenshots of the errors?
Edit: I downloaded the same modeler version and created a project with this module. The errors are coming from a navigation layout that doesn't exist anymore. To fix this, double click each error (which will bring up the page), and right click > properties > and change the navigation layout. Referring to my original answer, you will have layouts to choose from the Navigation Layout module. One thing to note, is if you change the layout, it may wipe out everything on the screen. Try and copy and paste the main contents of the page, change the layout, and then paste it back.
here is a screenshot of the properties menu for the page.
Someone in Mendix thought it was a really good idea to rename the layout placeholder from "Content" to "Main", without consideration for existing apps. This means that anything that refers to the placeholder by the name "Content" will fail.
You can fix this relatively easily:
For each page with an error:
(Repeat for each layout that is used by one of the pages with the error - I only had to do it for PopupLayout and Sidebar_Full_Responsive).