The screenshot of the shapes being gone doesn’t tell us much. It would be nice to know at what point in your process they disappear. Or to know what you mean by “really bizarre issues”. And what version of mGear you’re using.
I once discovered that some of the controlBuffer shapes were instances. Which is bizarre to me. I’m not sure which functions extract them as instances. But if your shapes are instances, then any edits you do on your rig, will edit the controllers_org shapes too. So maybe some bugs are occurring because of that. controlBuffer sticking around when outside of hierarchy of export selected - #6 by chrislesage
From a backup of a previous rig. You can export the shapes out from the controllers_org group and import them into your latest working file. Otherwise the data isn’t stored anywhere where it could be resurrected.
I don’t see how that would be any more or less intuitive. It’s a replace function. It gets rid of the old shape (including none) on all targets, and replaces it with the specified source.