Hi Jessica-
Congrats on your new client AND trying to teach yourself podiatry billing...not an easy task!
While I know nothing about billing for a provider in Hawaii, and about the sales tax requirement, I can offer one idea. If this is standard Medicare, I know that some MAC's will automatically reject an entire claim when one line or more on it is a HCPCS code that they don't cover, or should have been billed to DMERC, depending upon the situation.
Case in point, when my local MAC was WPS, I could bill certain non-payable HCPCS codes to them, along with payable CPT codes, and they would pay the CPT, and deny the HCPCS, which is what I knew would happen, and wanted to happen, so I could then bill the patient(per ABN, etc). But then my MAC changed to NGS, and I quickly found out that non-payable HCPCS codes on the same claim with payable CPT codes resulted in the entire claim being rejected. This could be what is happening to you, but because I have zero experience with the S9999 code, or your local MAC, I can't say for sure. Have you contacted Medicare for further clarification? That may be your best bet.
While I can't help you with this situation, feel free to message me if you need any other podiatry help. It is all I have billed for almost twenty years, and there isn't much I haven't seen/billed over the years. Except of course a DPM in Hawaii, and sales tax on medical care.