We decided to almost completely remove the AstarPath.active.UpdateGraphs() call to generate the mesh in places where the floor is generated. This helped reduce the number of crashes. Now we only have one place with a call to AstarPath.active.UpdateGraphs(), and the rest of the mesh is modified via NavmeshCut.
I also found a thread: GraphUpdate & NavmeshCut interaction causing errors
Maybe this is also related to a multi-thread race?
In a few months we will update the Unity version and the collections version, hopefully this will help.