That's exactly why Pence didn't get charged as well. Yeah, he had classified docs, but he surrendered them without any issue. Trump and his conspirator(s) on the other hand actively worked to deceive the US Gov't about the return of these documents.

If he had handed everything back, okay, there's nothing to talk about anymore, shit happens from anyone in a high level position (like POTUS, VPOTUS, SecDef, etc) where, like you said, they handled those documents on a daily basis for briefings, took notes, etc. to make decisions with. Sometimes things slip through the cracks, that's why there's the step of agencies saying "Hey, you still have some classified docs and we need those back." Complying with the request under the assumption of an honest mistake results in nothing occurring as a result. Pretending to comply and conspiring to further hide those docs, while leading your lawyers down a different path though is very much a violation of any good will the federal government is giving you.