Hello Liz,
we found solution for that.
We do baseline for program via process (works correctly for Baselines on milestone level) and than we are deleting values for baselined effort to avoid wrong summary on Hierarchy.
Baseline of Milestones on Program was request from customer which is using programs and linking Program Milestones against Project WBS and they want to see difference BL vs Curr not only on Subproject level but on Program level of WBS too.
Vit