After restarting the editor, any changes to the Gameplay Debugger settings will break debugging when used again.
The user can work around this by changing the Gameplay Debugger settings again after the restart.
RESULT
Navmesh debugging is missing, and is not listed at the top.
WORKAROUND
Change another Gameplay Debugger setting, and it'll start working again.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-51600 in the post.