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IMO, the best you're going to be able to do is to use an Estimate (New > Estimate) for each milestone. They need to be dated, but, since an estimate is a non-posting transaction, they will not impact your financial statements until you convert them to an invoice. You can create an estimate for each milestone and, once the milestone is achieved, click 'Create invoice' on the estimate and your client will be billed. Also, you can see their yet-to-be-achieved milestones by running an Estimates by Customer report.