Caesar II is a computer program that will simply analyse the data you have entered in the input. If you have entered a certain temperature case then it will calculate the Sh value for it and use it in the sustained case analysis of B31.3 (if it is the lowest value of Sh).

As Dave Diehl said, the sustained case is designed to check the pipe does not fail under primary loadings at any time. It therefore has to consider the Sh of every temperature you enter, as you have implied that it could come under these conditions at some point in its life cycle.