I have an existing temporary reference in an existing loaded file that looks like this in TES4EDIT:
[REFR:1A01CA2C] (places cobAlsShelfUCGreen "Alchemical Ingredients" [CONT:02002A7A] in GRUP Cell Temporary Children of BattlehornCastleForgottenPassage "Battlehorn Castle Grotto" [CELL:1A00605C])
What I wish to do is to create a new patch file that has a reference that is the same (same position/rotation/etc) but with a different object being placed (cobAlsShelfUCGlass).
How do I do this (I am guessing that since this is a temporary reference, I wont be screwing up my save game by doing this change)

Also, how do I (in the CS) create a copy of an existing container that I can then edit and where it has the same name and form id so it will replace any existing instances of the container with my edited version?

Plenty of stuff out there about creating new things but not all that much about how to make a copy of something that already exists in a way that lets you replace the existing item and have references and stuff match up.

I imagine the easiest way would be to ESMify the plugin in question, go to Find and Replace and replace that reference with the one you'd like, which keeps the properties the same. Save the ESP and then un-ESMify the plugin.