The term schedule in this case does not refer to the time-based models that have been discussed previously in the book but,rather,to a listing of costs to be used as a basis for billing throughout the project.
这个句子主干是这样的, But并列了两个to:
The term schedule in this case does not refer to ... but to ...
the time-based models that have been discussed previously in the book
这一部分有一个定语从句,关系代词在从句里面做主语。