MILESTONE BILLING- Mile stone assigned to multiple sales orders

Hi,

My user has sales order in which he has used Mile stone billing

The Billing is being done in two shots - 60% once and the second time 40%

60% has already been invoiced and the 40% is creating a problem and they want the sales order to be closed

In one of the custom reports- it says that the 40% (mile stone number) is assigned to multiple sales orders and so the sales order cannot be confirmed

I am totally new to SD and so request to kindly explain high level concept and also provide the solution

Thanks,

SS