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On successful checkout there is an option to Download PDF which is the PDF of the Sales Order. Where do we define the Advanced PDF template this uses?

SuiteCommerce uses the same template that the NetSuite UI uses

So if you want to change it you will need to customise the transaction form and change the printing template in the form there

Or set your custom PDF template as the ‘preferred’ option in *Advanced PDF/HTML Templates* 

(Of course, you can choose to use a different sales order form for the web store by changing it on the web site setup record, but _that_ form will use whatever PDF template is associated with it.)