I accidently linked two accounts together with Gmail multiple account sign-in.
When I go to https://www.google.com/settings/security there is supposed to be an option about multiple sign in under the password there, but it is not. The (old) Google help FAQ page for how to do this now 404's.
I was having this problem, too: I logged into my Gmail from my sister's Gmail without logging her out first (oops) and it linked our accounts. So, just hit sign out on any of the accounts, and it will make you re-log in to all of them. Then just don't re-log in with the account you wanted removed (or log everyone else out first by logging just one Gmail account out; it logs all Gmail accounts out simultaneously) and you're good to go.
The way you do it is in the right corner drop down where you would go to switch between accounts, click on "add account" (as if you were going to add a third). At the bottom of your list of accounts to the left it says "add account" and the right it says "edit". Select "edit" and all you have to do it "x" out the one you want to remove.