Hi Kartik,
First we need check whether it's logical for business to sell all or most of the materials to same sold to party. The data which is coming to APO is on the basis of data available in sales order/delivery. Now in SO you have both sold to and ship to. In delivery also you have both but in this case ship-to driving factor for the document (though sold-to is available in partner functions).
As you mentioned yourself that master data is being changed frequently, this of course could be one of the reasons for discrepancy depending upon what has been changed/when it has been changed. Are you CIFing the changes to APO on regular basis to APO?
Also check why such frequent changes are being done?
Regards
Rahul