The issue is that the dev team made some poor choices in how they implemented achievements. In an ideal world, it probably wouldn't have caused any problems, but because of unexpected failures in the system, those choices have apparently made it so that different components of the achievement system can be out of sync with each other, and correcting those inconsistencies is apparently difficult. Most likely they don't know which system to trust, so they can synch the values between them. Or worse, it may be that they can't universally trust any of them, and will have to write a complex function to compare the different values, and determine what to set them to based on the particular mixture of values.
If they write this function wrong, they'll probably mess up the entire database, awarding achievements to people who haven't completed them, and removing them from people who have, in an inconsistent fashion. They could just roll it back should that occur, and that's probably what they're testing behind the scenes, and why it's taking so long. They have to query the database, try to figure out what's wrong, modify their algorithm, run it on the whole database, then examine it to make sure it fixed the problem without messing anything up. Considering that they have millions of accounts, that's a lot of data to sort through.
They don't want to push a fix to the live version of the game until they're sure it's not going to mess people's achievements up even more than they already are.