I'm wondering how class skills work that have the wording, "gains a +1 morale bonus on skill checks. This bonus increases by +1 for every x levels beyond xth," when you gain levels in a second class.
For instance, I have a character with the Rake Rogue archetype, who has the class skill Rake's Smile, which reads: "At 3rd level, a rake gains a +1 morale bonus on Bluff and Diplomacy checks. This bonus increases by +1 for every 3 levels beyond 3rd."
However, for his 6th level, he switched to the prestige class Noble Scion after being granted noble titles, so his status is Rogue: 5, Noble Scion: 1.
He's 6th level now, but only 5th level Rogue. So would the Rake's Smile rogue class skill give a +1 morale bonus to those checks, or a +2 morale bonus?
Just to clarify the term class skill has a specific meaning in pathfinder. Each class has a list of skills that are considered class skills. If you have at least one skill point in that skill you get a bonus of +3 in addition to the number of points invested in the skill. Rakes smile is class ability, not a class skill.
Leclomenia is correct so your bonus would be +1.
What they said.
This prevents making the obvious pattern for character creation "take a level in every class with a level-scaling class ability". There feats that exist solely to alleviate this feature in specific circumstances (e.g., Shaping Focus, Boon Companion). There is even a single prestige class, evangelist, that does allow you to continue to level other class abilities when you take levels in it, so if you want to see what the wording would be like for something like that, check it out.