Any refund check you get from the state is going to be considered paid to you, so might as well deposit it. It won't have any major impact on your ability to dispute an adjustment, it'll just be factored into your overall tax situation. If you thought you were due $1200 and they sent you $1000 instead, if you can get that fixed they'll just send the missing $200. You don't have to undo / cancel the "wrong" $1000 check to get the full $1200.

As for why the refund amount changed, that's harder to guess. When did you file? When was your return accepted and refund check sent? Government bureaucracy can sometimes cause communication to lag behind money moving around. I've had explanation letters show up a couple weeks after the check. But if it's been more than a few weeks since you got that lower refund check, that feels like time to start pushing harder on them for answers.