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The IRS will not release a levy until the amount they see as due is paid. You can oresent your calculations to the IRS and ask them to adjust their findings. They will probably not agree.
I would take a slightly different approach to this. I would pay the levy so it comes off the open status at the IRS and then present your calculations asking for a refund of the difference. The business will be able to continue operating without this hanging over them.