Did a chat with turbotax support/expert. They suggested I delete all 1098s and re-enter them manually in chronological order. For me it was 4 loans, original, refinance 1, sold/acquired mortgage, and refinance 2. I still had to change the 1098 box 2 to $0 for all but the current one. This seemed to work for Federal as well as CA state. Without the chronological order the CA state added them together. I don't think its technically correct to set box 2 to $0, but it does seem to work around the issue.
