Yes. The amended tax return is a separate return. Filing an amended return assumes that the original return is complete and any refund due has been received.
Based on your question, it seems that New York has processed your amended return (with a balance due) but has not yet processed your original return (with a refund).
To clarify: did you e-file your original NY tax return? And if so, does the filing status on the Tax Home page in TurboTax Online show that it was accepted?
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