To change a partner in a salesorder - shipto in my case - I just had to fill in the partnerchanges table. There is no need to enter the partner information again in the partners table which I was populating. I understood this only after debugging the update sessions of VA02 and the BAPI concurrently. My BAPI call was trying to insert the soldto and shipto again resulting in a SAPSQL_ARRAY_INSERT_DUPREC error.

Anyway, since there I searched extensively and found no information on how or what fields to fill to change a partner in a document I thought I will put down the info I gathered. Here is what I found, hopefully it will be useful for someone else.

1. PARTNERS table : Fill this table with any new partner function(s) that you want to associate with the document. For example, you created a salesdoc and now want to associate a salesperson to it. Enter the partner details in the partners table with the appropriate partner function. Do not enter any partner functions already associated with the document in this table

2. PARTNERCHANGES table : If you want to update any of the existing partner functions associated with the document enter the old and new values with 'U' in the updateflag field. You can also disassociate any non-mandatory partner functions with a document by entering the values with a 'D' in the updateflag field.(Disclaimer : I have not tried the delete/disassociation but this is based on the what I saw during the extensive debugging sessions ).