Your question is not very much clear. But, here is my response base on what I understand from your question.
If your application is handling all the affiliation then why do you need AWS API in first place as it will promote products on Amazon only. if your web application is independently offering the affiliation program to promote your web products not yours then I don't think that you need to have AWS API.
However, if you want amazon server or considering AWS API as deployment server and want to deploy your APIs on amazon deployment server, then I see no reason why it wont work.
Thanks & Regards.
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