"Vanishing Point" is the Hoshi Sato moment of the season. Early in the series she was the character who was most uncomfortable entering into an ongoing space assignment. She was the one who panicked. (That's what "Fight or Flight" is all about!) Yet she was also the linguist, the predecessor to the more vivid imagining of Uhura in J.J. Abrams' Star Trek. Without her it would have been a lot harder for Archer and his crew to communicate with aliens. In the second season, notably the Trip-centric episodes "Precious Cargo" and "Dawn," Hoshi is no longer the center of that particular aspect of the series.
Instead we get this episode. It's ostensibly an extension of the skittishness the crew feels about transporter technology, which even when taken for granted in other incarnations of the franchise from time periods later along the scale could cause panic (the accident in The Motion Picture, Barclay's adventures in "Realm of Fear"), though not quite to the point where it was a problem for Archer's gang.
Hoshi faces her continued inability to feel completely comfortable in a scenario that's straight out of a nightmare, stemming from a forced trip through the transporter that ends up making her fade away, her colleagues increasingly unable to hear or see her.
To the extent that it all seems a little perfunctory (like Reed, Hoshi can sometimes seem a little uninspired, even one-dimensional, and while this is an interesting episode it doesn't say anything new about her, which again proves that the writers had other characters on the brain this season), it still mostly works.
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Memory Alpha summary.