Hi Nathan,
Thanks for your question. What the copy-paste function does in the background is saving a small subproject (Mimics or 3-matic) and then importing it again. This is significantly faster than exporting and importing to and from non-Materialise formats. Would this be possible within your workflow? If at all feasible, try to remove all other objects from the projects before saving and importing. In Mimics, you can use the save_subproject function:
mimics.file.save_subproject(r"C:\Users\jdeckx\Desktop\Temp\test.mcs",[mimics.data.images.get_active()])
I hope this helps!
Julien