Question

How to set the primary key for the existing dataset column in the Invoice Document Definition? For example, in PurchaseOrders and PurchaseOrdersItems dataset. 

Answer

The default datasets structure is not editable in the Invoice document definition. It is also not possible to delete default datasets. 
However, it is possible to create a custom dataset and set a primary key there.

The default dataset structure is described in the following article of FlexiCapture documentation.