Use sorting of navigation modifiers.
To enable it, check Project Settings > Engine: Navigation Mesh > Sort Navigation Areas by Cost
When working with Nav Modifiers in a level that contains objects that have a custom Nav Area class, the prioritization of the modifiers is not consistent.
If you notice in the attached project, some of the objects are affecting the yellow area of the Nav Mesh, while others are not, and this priority changes intermittently.
The thread contains images of the desired setup and the actual result.
Found in 4.14.0 CL# 3195953. Reproduced in Dev-Framework CL# 3221683 and 4.13.2 CL# 3172292
Result: Notice that the objects containing different nav area classes are not always affecting the yellow modified area of the nav mesh.
Expected: The objects with the other area classes would be prioritized over the yellow modified area, or there would be a setting to determine prioritization.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-39630 in the post.