I suggest that you touch the areas of the dough around the bubbles. If those areas are firm, then I think you should be able to safely puncture the bubbles if you want to age the dough even longer, and return the container to the refrigerator. Glutenboy's dough is capable of long fermentation windows because the amount of yeast is modest and the dough balls are small. This allows the dough balls to cool down quickly and, so long as the refrigerator is also cold, the dough balls can be held for many days. Glutenboy's dough also uses 2.5% salt. While not overly excessive, that percent of salt might slow down the fermentation activity by virtue of its affect on the yeast.