If AMD Warranty is voided due to those scratches then Micro center Retailer is responsible in replacing your CPU since they were the ones at fault for damaging the CPU and voiding your AMD Warranty.
Now if those scratches are superficial and not deep then possibly the Thermal Paste will cover them completely and you will still be able to use it. But if they are deep then you may have heating issues when you install it.
I would have Micro Center Retailer replace your CPU since they were the ones that damaged it in the first place.
To check to see if those scratches voids your AMD Warranty I suggest you open a AMD Warranty Request (https://www.amd.com/en/support/kb/warranty-information/rma-form) and see what they say. If they report back that the Warranty is voided after uploading your photos then you can take that back to Micro-Center for replacement as proof that they are responsible.