The problem is a result of two things:
Sounds like the problem can be solved by just not copying bStaticRuntimeNavigation
Result: Freshly opened map's WorldSettings.NavigationSystemConfig.StrictlyStatic is already set to true
Expected: every map's WorldSettings.NavigationSystemConfig.StrictlyStatic is independent
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-91171 in the post.