Chucking things in boxes was an excuse for harried staffers throwing everything into boxes and taking them to Joe's basement as Mike Pence's team kicked them out of the office. The documents found their way to this office two years later. Someone decided that these documents belonged there, rather than where they had been before.
The timing of the revelations is also a problem. I think it is pretty transparent that they kept the discovery secret because of the election. But, when that initial discovery was reported upon, the subsequent discovery in Joe's garage had already happened a month before. Why the administration would admit the November discovery, and not mention the subsequent December discovery at the same time is mind boggling. The drip, drip, drip of revelations just makes the whole thing more suspicious.