The "BioReplicate" column that you sometimes find in Skyline documents is actually a custom annotation.
You can define custom annotations in Skyline by going to:
Settings > Document Settings > Annotations
The Group Comparison tutorial walks you through defining that annotation, and then making use of that annotation when defining a Group Comparison:
Calibration Curves in Skyline never do anything with the BioReplicate annotation. Whatever values you may have set on those replicates never had any impact on the slope and intercept that Skyline calculated for the calibration curves.