I have found a minimum spanning tree (left figure). Then I have applied some modification:
- The edge
A-B(red) was added, - The edge
C-D(green) was rewritten toC'-D.
Edit. I don't delete the vertices.
- Steps 1-2 can be repeated more that one time for different edges.
Question. Is there a math term for an obtained graph (right figure)?

Well...it's no longer a tree, so I guess the best I can say is that it's a spanning subgraph. I'm not sure whether your "modifications" always preserve the property that the new graph contains all the vertices. If not, then you can just say "it's a subgraph."