Ultimate Magic says on page 14:
If an archetype replaces a class ability that is part of a series of improvements or additions to a base ability (such as a fighter's weapon training or a ranger's favored enemy), the next time the character would gain that ability, it counts as the lower-level ability that was replaced by the archetype. In effect, all abilities in that series are delayed until the next time the class improves that ability. For example, if an archetype replaces a rogue's +2d6 sneak attack bonus at 3rd level, when she reaches 5th level and gains a sneak attack bonus, her sneak attack doesn't jump from +1d6 to +3d6—it improves to +2d6, just as if she had finally gained the increase at 3rd level. This adjustment continues for every level at which her sneak attack would improve, until at 19th level she has +9d6 instead of the +10d6 of a standard rogue.