Doing Build Geometry breaks Build Paths (navigation) permanently

Hey everyone,
Three days ago the following worked for us with expected behaviour:
Have an empty level with a Nav Mesh bounds volume in it with correct nav mesh.
Click Build → Build All Levels
The Nav Mesh stays as is.

Since two days we have the following issue:
Click Build → Build All Levels
The nav mesh is gone and we can do nothing to get it back.
Including Build → Build Paths not working anymore.

Unfortunately this also means our packaged games do not have a Navmesh anymore, since packaging the game seems to trigger a similar process at least in our specific project.
Is there any way to disable that process, so that we can at least again package our game with a navmesh?

We have isolated the issue to:
Build → Build Geometry breaking the nav mesh permanently.
We have this issue as a team, three team members are already affected.
This happens in new Unreal Project with empty map for everyone.
Is there anything we can do to fix this?

The best we could do so far is using a Nav System Config Override actor in our map.
This fixed: Build → Build Geometry breaking the nav mesh permanently in editor.
However, the packaged game still didn’t have a Navmesh.