Is it a good practice in C#.Net to launch application B from application A, then close application A? Could there eventually be thread problems / bug?
There isn't any guidance on such a thing.
If you start a new process (Application B) from your Application A, they are considered completely separate.
If you then terminate the Application A process, it would not interfere with Application B.
The only issue I can see is if Application B is trying to access files that are still open by Application A (while it shuts down).