I had a few products that I thought were borderline infringement so I will just remove them. The Attestation for the sale of branded or trademarked products link in the email goes to a form you need to fill out. For me I will just check off that I have deleted the products. If you have documentation that you have the right to sell branded products then you would have to show them proof of that.
I don't think it has anything to do with Shopify payments. Either someone reported your website or Shopify stumbled upon it and noticed that the item you are selling is branded with a trademark. They want to make sure that you are authorized to be a distributor for that product. If you are not then legally you are not allowed to sell it and the item has to be removed. That's how I understand it.