Characters' navigation relevancy is controller via bCanAffectNavigationGeneration flag. It's not obvious, especially that toggling this flag in editor mode doesn't affect navmesh. In CL#2926616 I've added a piece of code that mostly addresses that.
Upon PIE, the Can Ever Affect Navigation option is being reset on the capsule component of an empty character. Dragging the empty character into the level, setting the option to true, and then playing in editor causes the option to be reset to false (which can be seen in the details panel).
Found in 4.10.4 binary. Reproduced in 4.11 Preview 8, and Main CL 2917742.
1. Open the editor
2. Create a new level
3. Add a Nav Mesh to the level
4. Add an empty character to the level
5. Under the capsule component option in the details panel, check the Can Ever Affect Navigation option
6. Simulate or PIE
Result: The Can Ever Affect Navigation option has been reset.
Expected: The option would remain checked as it was set in the editor.
Head over to the existingAnswerHub thread and let us know what's up.