The foliage instanced mesh, as well as ISM and HISM components both appears to be unable to export navmesh data for generation once we introduce a change in the contents. This error only shows up in a packaged game,
This was reported and tested in 4.22.2 (CL-6574378) and reproduced in 4.23 (CL-6836100)
You will need a Source Build of the Engine for this issue
Results: Once you introduce a change (eg Update Transform) in the instanced mesh tree the navmesh will ignore the instanced meshes, so the AI will not be able to navigate properly in these areas.
Expected: The navmesh will be properly regenerated around the ISM (foliage) exactly as it is happening in the Editor.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-75841 in the post.