Does this look bad?

Does it look bad going from taking 2 AP classes and 3 Honors (sophomore year), to taking 3 AP classes and 1 Honors?

Not necessarily.

Will you still have all the cores you need for the colleges you are aiming? Will your guidance counselor check the box indicating you have taken the most rigorous course load available?

Colleges will understand if you are taking a class not offered at an honors or AP level. They will understand if you need to get a gym or other school or state required class done for graduation. They’ll even be understanding of schedule conflicts and balanced choices, provided there is rigor where it matters. Go over your plans and schedule with your guidance counselor, who is in a better position to advise you in the context of your high school’s options and offerings.

It really depends on the exact classes you will be taking.

Sophomore - AP Environmental, AP Stats, Honors Trig, Honors History, Honors Lit

Junior - AP Calc, AP Physics 1, AP Lang, Honors Psych

I mean my school doesn’t have honors classes so I don’t know about those, but you’re going from two of the easiest AP classes to three of the harder ones so I doubt any college would fault you

You’re not taking honors US history? Dont forget a foreign language.
Your schedule +history honors + foreign language would be mist most rigorous.