Business Filing in multiple states

An S Corp operates in several different states every year, but the states vary year over year. For example, 2 years ago they had some income apportioned to California (2023), but last year they had no operations in Virginia and the preparer didn't file a California return (2024). I was under the impression if you weren't going to file in a state anymore you need to check the "final return" box to avoid the state reaching out and charging late fees/penalties. Am I the one misunderstanding the situation or did the previous tax preparer (2024) make a mistake?