I'm sorry, but most of this is just plain incorrect information. The alcohol helps against certain types of bacteria, but certainly not "almost everything."
There are tons of different types of lacto, pedio, brett (aka wild yeast, which there are more than just brett), and acetobacter. All of which can continue to eat the complex sugars in an alcohol-rich environment. Check out the "Post your infection" thread for proof of that.
Yes the acetobacter will start producing vinegar, but if it's not the style he's going for, or if it's some really funky bacteria or wild yeast, then it's possible anything will be bad for the beer.
OP, as others have said, especially Gavin, the problem is the amount of headspace in your secondary, mixed with that you need to either soak the cacao in some kind of strong alcohol (typically done in vodka because it's the most "neutral"), or baked prior to adding them to secondary. If you did purge, then it's likely more of the latter.
After they have been in the bottle for 2-3 weeks, start checking the carbonation. If it's where you are expecting it to be, then it would be advised to put them all in the fridge. It will significantly slow the process, but you would still have a time limit (in other words, you don't want to be aging them for a year or anything).