If Turbotax does not fix this issue specifically related to NYS returns, there is an interesting on-line advise from Turbotax dealing with refinanced home loans with multiple 1098s. This guide will result a single 1098, which may eliminate the current glitch on NYS return. Read this as REFERECNE only as it just came up in my search.
https://ttlc.intuit.com/community/loans/help/what-do-i-do-if-i-have-multiple-1098s-from-refinancing-...
