Currently, when you use the "Option Assignment" menu option, all contract quantity for that leg of the trade will be used in the assignment. For example, if you have 5 Puts but you receive notice from your broker that 2 were assigned, then if you try to use the Option Assignment then all 5 will form part of the assignment when obviously you only wanted 2 to be assigned.
The workaround is to wait until you have handled the other 3 non-assigned Puts of the leg. You could roll those 3 Puts thereby splitting the trade into two transactions. One for 2 Puts, and one for 3 Puts. You can then easily use the Option Assignment on the 2 Puts that were not rolled.
Another alternate workaround is to Roll the 3 Puts to the SAME EXPIRATION day as it is already set, AND do that roll for no cost. In the Roll dialog, just change the leg quantity in the "Closed Transaction" and also "Rolled Transaction" tables. This will split the transaction into two separate transactions then allowing you to use Option Assignment on the 2 Puts.