There is no functionality for switching Primary and Alternate BOM.
Instead create a Common BOM across Org hierarchy
You can try this work around. Just make the alternate routing as your primary routing using the switch option. Now list the difference between your primary and alternate bom, using ECO (incase you are using engg module) make the change in your primary bom to match those of alternate bom and vice versa. Thus the your issue should get resolved using this.