I have some that have done that for the last three years. The first year I cut off the flower stalks as soon as they emerged and I did the same this year. I did let them die back completely before harvesting and they stored reasonably well, but not as long as others that did not flower.
Last year I left one flower on and harvested seeds which I germinated and planted this year. They are at least several weeks away from harvesting, but the tops are much smaller than the original shallots.
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