Hi ahandford,
I have no idea about your setup, but typically, use the cache of the Rigid Body tag and “bake” all the parts. Go to the frame where you like to have the copy from. Then while the Cloner is selected, use the Object Manager> Object> Current State To Object. The New copy should be in the way you like to have it. I assume you don’t like to have all the single objects. First, delete the Rigid Body tag of the copy (do that before you do anything else!)
Then, while the new copy-parent is active, use the Object manager. Object, Connect, and Delete. Now all parts are on the object, well two, as the jar didn’t need extra treatment, it can be cmd+dragged if a copy is needed.
If you have no use of the original Cloner, you could do the same, but instead of the current State to Object, use the C key while the Cloner is active (cached, of course, just to be safe)
In case that you encounter any problems, please let me know, and share a small scene file (project file); thank you.
Cheers