Have you been to the Paizo Account Synchronization page on the Fantasy Grounds site and clicked the "Send Purchase Info to paizo.com" button?
I've found that I have to click the Retrieve button on that page when new modules are released (when I've already gotten the PDFs from my subscription here) in order for my FG discount to show up, so I suspect you may have to do similar going back the other way.
|Sam Phelan Customer Service Representative|
Unfortunately I'm not too familiar with this process! Ionejedi likely has better advice as someone who uses this feature. I know that the system works generally in providing discounts for the equivalent PDF, so if your accounts are linked correctly and you have done the step above detailed by Ionejedi, and the PDF does not appear nor has a complete discount applied when added to your cart, please let us know! Thank you!