To solve the problem, you can call the bake navigation code after the level changes.
Bake Navigation Inside Unity Editor
This code works similar to what is in the Unity Editor. Just make sure your Navigation Static object is enabled before using it.

The NavMeshBuilder
class will allow this. In the code bellow.
using UnityEditor.AI;
...
public void Generate()
{
GenerateLevel(); // for e.g
NavMeshBuilder.BuildNavMesh();
}
Bake Navigation in Runtime
To bake in runtime, you need to download the necessary NavMeshComponents.
The component's will give you a NavMeshSurface
component. It does not require static
navmesh and works locally. Add component to all of your game ground's then put them in a list as the code bellow. After each run of the game, it is enough to BuildNavMesh
all or part of them.

public List<NavMeshSurface> surfaces;
public void Start()
{
GenerateLevel(); // for e.g
surfaces.ForEach(s => s.BuildNavMesh());
}
Also this tutorial from Brackeys will help you so much.