There is no missing chapter that explains what happened but I will
The missing chapter
You might have heard that there is a missing 18th chapter that explains what happened to the girls, you might have read a discussion about it. You might have read a summery or even obtained a copy of said chapter; if you have then you would know that the chapter basically tells how the girls entered into a crack in the rock and into a place suspended in time, thus Hanging Rock is actually a rock hanging in time as well as space. If you think that this answers anything I advice you to stop reading and go immediately to a psychiatric hospital and demand a thorough examination of your head.
The missing chapter does not answer anything at all, indeed it demands a thousand more question than the one question about what did happen to the girls. So although I don't deny the existence of an extra chapter I completely refuse the idea that it explains what happened. Any editor worth his name would cut several chapters from any book, but no editor in the history of books have cut the final chapter that answers the mystery.
But we are told that the chapter was cut on the publisher's request. No publisher in the world would ask a writer to make their book more ambiguous and without a proper satisfying ending for two main reasons: an ambiguous book without a satisfying ending would suit less readers than otherwise and more importantly this interferes with the authorship of the book.
So why was the chapter cut? To understand the problem of the chapter we have to remember the history of F&SF (Fantasy & Science Fiction) which started as a completely different industry than book publishing even to the point of using different paper, different fonts, different covers, different marketing and pricing. Readers of more traditional books looked down and despised the growing popularity of F&SF and although certain elements of fantasy (like those present in the missing chapter) were once accepted as a literary device to represent the metaphysical part of life by the 60's such elements were completely exorcised from traditional books.
The publisher advised Joan Lindsay to cut the one chapter with fantastical elements to preserve the purity of the book and make it acceptable for the readers.
What really happened
In a nutshell nothing happened because none of the girls (Miranda, Marion, Irma, Edith and Sara) were real, they were all figments of the imagination of a girl that I will call ur-Irma, she is not the same as Irma but shares many of her physical aspects.
Ur-Irma like the girl in Saki's The Open Window is a specialist in making up stories and she is actually our narrator, a highly unreliable narrator that weaves stories to hide a single important fact: she has lost her virginity. That is it, that's the whole story: a girl losing her virginity and becoming a woman.
Miranda represent the beauty (both of body and spirit), Marion the philosopher, Irma the physical part of the girl, Edith the child and Sara the tragic self-pity. Ur-Irma has parts of these five girls in herself, she is not as beautiful as Miranda or wise as Marion or childish as Edith or have suffered in her short life as Sara, she is a real girl while those four are aspects of her personality.
You probably want to know what exactly happened, unfortunately I can't tell you that because ur-Irma is a liar who greatly obscured what really happened to cover her loss of virginity. Nonetheless we can infer some things: ur-Irma left the picnic and went walking up the rock, where she met a boy and something happened between them that shocked her and forced her to retreat into a childlike state, suppressing her beauty, wisdom and physical self. After a week she met the boy again and lost her virginity becoming a woman.
Twice we are told by the doctor quite explicitly that Edith and Irma are “intact.” In the whole story there is no single explicit fact more clearly pronounced than the intactness of Edith and Irma, or so does ur-Irma want us to believe, because she has lost her virginity at Hanging Rock.
When she visits the school she is clearly a woman looking at children who wonder what happened to their friend who looks so different now, none cries the loudest than Edith. But what about Sara, well many children left in boarding schools have similar feelings to orphans, feelings of abandonment and loneliness, this manifested itself in Sara, who is an orphan suffering too tragically even not allowed to visit the rock.
As ur-Irma becomes a woman she understand the limits of her beauty and wisdom, the need to restrain the child in her and leaves self-pity behind her at the school as she travels to rejoin her parents.
I leave the other parts (e.g. what about the governess, who is the boy, etc) for you to figure out.