Custom Number before ship confirm

Hello,

We are trying to find the solution for below business requests, please advise if any one come across like this and got some solution.  

 

We create IR/ISO, and inventory got transfer from one warehouse to other warehouse while ship confirm of ISO .

 

But before doing ship confirm we got some number from custom and want to store those somewhere, so that that number can be display on customer(AR) invoice.  The issue is, we may have two diff number for same lot an item

 

Like item X lot B and Number is 123,

          Item Z lot C and number is 123