I think I misunderstood your original question as indicating that your amended Form 1099-SA had all zeros and I now think that you instead meant only that the your Form 1040X showed zero changes. In that case your corrected Form 8889 would not have zeros on lines 14a, 14b and 15 but would instead have corrected numbers reflecting the corrected amounts from the Form 1099-SA. You should have included that corrected Form 8889 with your amendment.
It's entirely correct that your Form 1040X would have no changes shown on lines 1 through 17 if both the original and the corrected Forms 8889 indicated that the entire amount was used for qualified medical expenses, resulting in $0 on line 16 on both. The purpose of the Form 1040X was to explicitly show that there is no change to your tax liability, to provide a place for your explanation to that effect, and to provide a place for your signature. So it seems that there is nothing wrong with what you sent (unless you failed to include the corrected Form 8889) since the only purpose was to correct lines 14a, 14b and 15 of your Form 8889.
I think I would reply with copies of the original and corrected Forms 1099-SA and Forms 8889, clearly marked as such, and explain that your amendment was only to correct the originally filed Form 8889 which resulted in no changes to anything else on your tax return since both the original and corrected Forms 8889 showed $0 taxable.
