From the moment you copied your original wallet, they both began their own separate lives.
Encrypting one using a passphrase won't affect the other.
The only thing they share is a pool of x (with x=100 by default) pre-generated addresses.
This basically means if you click 100 times on "create new address" in each of those, you'll get the same addresses "created".
This is false. Encrypting a wallet deletes all unused addresses from the pool and generates new ones. This is to reduce the potential for theft if someone obtains the unencrypted wallet (and in fact that risk is eliminated entirely if, after encrypting the wallet, you send all your coins to a new address and never reuse your old addresses).