Good Day Ken,
I seem to have understood the issue you are facing. Note that A Shift Day Program is used in 2 Sub Modules viz.
1) Shift Pattern
2) Shift Planner.
I understand from your query that you have removed its usage from Shift Planner. What about Shift Pattern?
IF not, remove the shift programs usage from shift pattern and you will be able to delete that shift day program.
Hope my reply enlightened your concern.
Regards,
Abhishek Nair
Lenvica Support