Dear @shahramshokouhfar,
I answer also on the forum on top of your email.
SOFA indeed integrates the API for topological change. This can be noticed in all scenes in the folder : examples/Components/topology/TopologicalModifiers/.
There you will find several volumetric mesh example.
Moreover, having the topology correctly updated when a cut occur is more advanced than element removal / adding. For industrial purposes, a good strategy could be a collaboration with consulting company like InfinyTech3D, who made nice demonstration simulation at our last SOFA Symposium. Let me know if such a connection if of interest.
Best wishes,
Hugo