When a number is transferred from the storage to the mill, the mechanism clears the number to zero (see Bromley 1998, p.31).
In the sketch, it is mentioned at various places:
However, from Bromley's cited article on p.31 left column, the final solution is different: This form of storage exhibits a destructive readout; following the read operation, all figure wheels will stand at zero, irrespective of the digit originally stored, and the number originally stored is lost. If it is desired not to loose the number, then it must be stored, as it is read, on another set of figure wheels. For this purpose, each figure axis of the mill of the Analytical Engine is provided with two figure wheels in each cage. It is not clear whether the saved number is returned back to the primary wheels once the number has been transferred, i.e. while the mill works, or the store colums just switches to the alternate set of number wheels.
Note that information is destructively readout with many types of storages, in particular core memory and dynamic RAM cells. However, the later solution was to provide one set of wheels for each ingress shaft, and write it back while the mill works, instead of duplicating the whole memory. With core memory, this did slow down the CPU, thus the memory was splitted in even and odd banks, slowing down the CPU only if two even or odd addresses where used in direct succession.
The ENIAC with its decimal shift registers would have had the same problem, but instead of shifting down to zero and counting, it shifted up circulary and counted the number of places shifted out on top. This would have been possible for the AE too, by turing the toothed wheel (indicated by 3 in Fig.1 of Bromley) a whole circle, and using the turn of the axis A (indicated by 2) instead. Clearly this would be done differently, once seen to be useful.