At the time Muffin was being dug up in the field, the paleontologists were having blueberry muffins and our "Muffin" was right next to the specimen that is now called "Blueberry" so both Muffin and Blueberry were named after their snack.
Time happened. The river plain was flooded and some bones floated away. Scavengers such as crocodiles had Muffin for lunch. Although few, there were some pterydactyls back then that could have flown off with a chunk. Asteroids. Speculation boils down to "we don't know".
We refer to it as being in "Paleo Time" (aka, things take eons to get done). In the case of Muffin, it was discovered in 2002 but there was an additional delay of about 11 years while the digging lease was renegotiated with the ranch managers. After that, it took about three years to get it to the Tate which was June 2016. Why does it take so long to do the prep lab work? It was big. We did not have much space in the Prep Lab until the Rex Annex was built and it could be worked on out there. I started prep in 2017. I did the database entries in 2022. I am slow. I do 3D as I go, (on Muffin and other specimens) and that takes time.
We know Muffin is a sauropod because the partial pelvis is that of a "bird hipped" plant eater, not a "lizard hipped" theropod meat eater. From there you go down the family tree. In paleo terms, Muffin "is distinguished by dorsal vertebra lacking cranial centrodiapophyseal laminae. Also, it is distinguished by elongate intrapostzygapophyseal laminae, dorsoventrally directed dorsal transverse processes that approach the height of the neural spines, and the distal end of the scapular blade being dorsally and ventrally expanded" (Weishample et al., 2004). So you might say we know that Muffin is a Haplocanthosaurus because of "the ratio of the neural spine to the transverse process" and the shape of the ilium.