Sapphire Warranty goes through the Retailer or Official Sapphire Seller that sold you the GPU Card.
The Retailer is the one that decides on what type of Warranty repair you will get. Whether it is a GPU card replacement, Repairs or equivalent Money the GPU is worth at the time of Warranty.
Basically you are at the mercy of the Retailer that sold you the GPU card.
If the Retailer asked you to change the fan assembly, make sure you have everything in writing in case you have any issues in the future concerning warranty and the retailer.
I know that Sapphire GPU cards have a new system to replace the fans called the Sapphire Quick Connect Fans. This doesn't involve disconnecting the GPU cowl to replace the fans. Just removing some tiny screws and that is it.