Sounds like you know the leaves are important in the manufacturing and transporting of energy back into the lily bulbs. However, as long as some of the stem is still alive, it can do some of the work. I'd just leave the plants alone until the tops die down in the fall. Your plants will develop stalks and leaves next year. If there's not enough stored energy, they won't flower - until the following year. Best wishes with your lilies!
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