I’ve noticed that mirroring controls/replacing shapes messes with the metadata and will end up duplicating the shape without replacing it. This is messing up hierarchies and ends up breaking entire chains, and in my most recent case the entire rig. I’ve also noticed that using any control not created inside mgear will break the rig as well.
Can you give more details? What version of mGear? What version of Maya? And look at the script editor output. If it isn’t finishing the operation, there is a good chance there is a warning or error.
In what way are you “using” the control? And what “breaks”?
If you are trying to mirror or replace while both the guides and rig are in the scene, perhaps you are getting a duplicate name error.