Hi there, Elizabeth! It does sound like the dough became a bit over-proofed. We haven't used the aliquote jar method in our baking adventures but there are more factors at play that need to be considered than just the level of rise you seen in the jar, such as kinds of flour used, the hydration of the dough, amount of preferment or sourdough culture used and if the dough is yeasted or naturally leavened. If you have an active starter (if using sourdough) and are controlling your dough temperature and other ambient variables, the aliquote jar isn't really a necessary step. 

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