Flag values in Brother's Keeper GEDCOM files are imported into attribute values. You may display the attribute value(s) using the Person Entry Attribute item. You may also use attribute values to filter people using the Attribute Text filter term.
The Brother's Keeper flag name is used as the attribute name. Brother's Keeper flags do not have any value other than the name, but GedSite attributes require a value, so GedSite sets the value to "Y".