In response to the 12C letter, do as they say and only return the 1095-A and Form 8962. I can almost guarantee there will be confusion if you send in an amended return that also includes more information.
In regards to the 1099-SA, I would be inclined to keep the record and not amend. If you receive additional notice from the IRS later this year, you could then address the matter. The 1099-SA will not affect any refund processing and can be quickly resolved with a response to a letter should you get an inquiry.
