After so many trial and errors, finally we found a solid solution for this issue.
The problem is due to existence of BSP Brushes in the scene. If you have them in your scene, all BP actors will be disappeared during the light/geometry building process. To fix this issue, you need to convert the brushes into Static Meshes or remove them from your scene and then do the process of light/geometry building.
BTW, we’ve tested this solution on UE5.1.1 and it works fine in this version.