Well, I'm not sure how much exactly was missed because I never read more than one or two of the originals. I'm under the impression that the original articles each had a chapter of the story, a small hex map, and a sidebar with creature stats, rules info, or additional background info.
Champions of Mystara reprints the narrative from issue 169 on (going by the list at http://www.mystaranet.jamm.com/vaults/html/prodlist.html#DraRef) but issues 153 to 168 are summarized in a single page. That means it's missing the initial introduction of the Hollow World and the Heldannic Knights, and some visits to places on the southern continent that were never mentioned agained.
Now, here's where it gets tricky - it doesn't include any of the maps or sidebar material, but it does have two books of material that didn't appear in the VotPA. One is a section of rules for building skyships, which includes deck plans and complete NPC writeups for the Princess Ark, and the other is an almost-as-full-as-a-Gazeteer writeup of the kingdoms of Sindh, Graakhalia, Yavdlom, and Ulimwengu. Since Sindh and Yavdlom were visited during VotPA, I assume the material from the sidebars (and definitely the maps) of those areas appears in the expanded country descriptions. Graakhalia and Ulimwengu weren't visited in the VotPA narrative, but are located just north of Sindh and Yavdlom respectively, so they might have been mentioned in the sidebars.
There are also a few miscellaneous bits that I assume were originally from the sidebars - for instance, the "new monsters" section includes the Night Dragon, Cestian Gobbler and Heldannic Knight, which I assume came from the sidebars for the early issues whose stories weren't even reprinted. And there's quite a bit of detail on the Princess Ark, which might have taken up a lot of the original article space or might be new for the box set. So I don't know if most of the sidebars eventually made it in, but scattered throughout the book, or if it was just a couple of things. (That's one reason I want to get all the original info - so I can compare for myself!)
As for maps, the maps of Yavdlom and Sindh also include a bit of surrounding area, so I'd guess that the maps from issues 168 (Sindh/Jaibul) through 173 (Hule) made it in, but definitely none of the earlier ones on the southern continent, or the later ones of the Savage Coast. Of course, the Savage Coast areas were covered in the Red Steel sets too, so there are maps of them available whether or not they're the same maps. But stuff like Cestia, as far as I can tell has never been covered since the original articles.
