Conquest of the Horde

Has anyone here been able to successfully patch up one WoW folder to Cataclysm, and keep the other one patched to 3.3.5? I'm thinking of trying out a Cataclysm server, but I've heard that the patches even affect the folder you're not using.

Advice is appreciated.

I have both cataclysm retail and CotH on this computer.
I launch Cataclysm via the launcher and it has never given me any updating nonsense.
Simply copy your Coth folder and move it elsewhere and do a new install for cataclysm.