Update
I just did the same lectures (its taken 3 days btw) on my own project and similar issue. Although it didnt shrink the Nav mesh this time it moved it below the level of my map.
Incidently doing this on a 30Gb dev folder hurts (Hence it taking 3 days as it took the best part of 4 hours to commit to github).
As a further word of warning, If you have any packs added to aproject (like starter content or something from the store) then you may have some issues.
I found it wouldnt fix up some redirectors because it could not find the items they related to. This is because unreal had already removed the Matrials or the mesh and the textures couldnt redirect as they still wanted them in the old place to do so.
To fix this.
DONT delete things!
First go though every single folder (sub folders included) and check for redirectors.
Click on the actual folder or subfolder and clear the redirectors.
Check the log to see why if any didnt clear.
Move the files back and then clear redirectors.
DO NOT move the files back yet as its likely other redirectors will need them and other files.
Repeat the above for every folder and after all redirectors are gone put back all the files you had to move and then clear the redirectors if any for those.
This will then sort out linker errors and prevent issues after deleteing the empty folder.
TLDR Fix up redirectors on Content doesnt always work right.