Since the second loop is the last thing you do, other than twist the string as a whole for correct length, couldn't you just untwist the second loop, untwist the two bundles back to the first loop, and then remake the string from there using more backtwists? I've done this before when the string turned out longer than I wanted, and then remade the string a little shorter, and it turned out fine. I won't say it was fun, but no worse than stripping off worn fletching from an arrow and then refletching it.
I agree with the comment above about cabling really being nothing more than a cosmetic issue. I had been making strings for about 20 years before I ever heard about backtwisting, but, as someone else mentioned, it's the kind of thing that might bug you every time you look at the string, as opposed to feeling great every time you look at it after you repair it.