When adding the "Musket Master" archetype, the "Gunslinger's Dodge" deed is not removed from the character. According to the "Steady Aim" Deed, it replaces "Gunslinger's Dodge.
I've attached an example character that has the Musket Master archetype. If you head to the Character Sheet, the second page of the preview shows the Gunslinger's Dodge still available.
Version 6.06.01 - Pathfinder Core Supplements set
Java Version - 1.8.0_91-b15 (Oracle Corporation)