It's common knowledge that if you get a bonus skill, but already have it, you simply choose a different skill to pick up.
But what if an ability says "You become trained in that skill, or you become expert if you were already trained."--do I get training in a new skill if I am already an expert in that skill?
Skills say "Each time after the first that you'd become trained in a given skill, you instead allocate the trained proficiency to any other skill of your choice—though if the skill is a Lore skill, the new skill must also be a Lore skill." Generally lower levels of requirements are included so I'd say yes as Expert is inclusive with Trained. For instance, if a feat had Trained in Athletics as a prerequisite and you were Expert in Athletics you can take it. The same would be true of gaining Trained in a skill you're Expert in IMO; you'd get Trained in another skill.
I don't think you would get to upgrade to Expert proficiency. Not by the rules as printed. The skill reallocation general rule is only for Trained proficiency.
I do agree that you don't have to waste the skill grant entirely. The feat does try to give Trained proficiency too, so you could use the general rule and get Trained proficiency in a different qualifying skill. But you couldn't upgrade something else to Expert proficiency.