Very short version: Because quantum.
Richard Watson, out-of-universe one of the Cyan developers and in-universe a member of the D'ni Restoration Council, has written about this. Note that the letter is written from an in-universe perspective:
Many of the interpretations of quantum theory say that until a state of matter is observed, it exists in many states simultaneously - it creates a bizarre "probability wave" that contains all of the possible states of that matter. Therefore, as was proposed in Schrodinger's famous cat analogy, bizarre things happen on the quantum level that allow things like Schrodinger's cat to be both alive and dead at the same time, until one ov the states of observed, locking it in a single state, and collapsing the "probability wave."
What the D'ni seem to have concluded (proved?), is that those waves don't actually cease to exist altogether, instead each possibility continues to exist in an alternate quantum reality (read "parallel universe"), until a state is observed in that quantum reality, and the possibilities not observed in that quantum reality continue to exist in still another, and so on ad infinitum. This makes the universe infinitely complex, with every possible quantum combination since the creation of the universe existing in a quantum reality somehere (even the "unstable Ages"). The Books somehow allow observation of (thus the locking of) and travel to those quantum realities.
So, you can make "unobserved" changes (probabilities that haven't been locked down by description in the Book, or by physical observation in the Age itself) without forcing the Book to link to a new quantum reality.
This is why being careful of contradictions is so important. The problem with contradictions is that the Book attemps to link to a quantum reality that matches a contradictory description, and the closest thing it can find is usually fairly unstable.
"What about the changes [Catherine made to] to Riven? You still haven't answered that."
The changes made to Riven near the end of the Book of Atrus (pg 268 in the hardcover edition), were a collaboration between Anna and Catherine. Anna's main contribution was probably keeping the Book free of contradictions. Catherine's intuitive (but D'ni rule-breaking) style was so bizarre that earlier Atrus had claimed that her Books wouldn't even work - yet they did.
The daggers which mysteriously appeared around the island, and the lava filled fissures were made possible by her odd style - which I cannot explain. And although Catherine and Anna intended for the lava filled fissures as part of their plan to rescue Atrus while still leaving Gehn trapped in his Fifth Age, the Star Filled Fissure was not intentional or anticipated.
To me, it remains the most mysterious object in all the D'ni histories.
TL;DR: You can edit things which have not been observed and which were not previously mentioned in the Descriptive book, without breaking the link. Also, Catherine and later Yeesha do weird things with their writing and break the rules.
In response to a fan query, Watson had this to say:
I was reading BoD the other night and something finally made sense to me.
When you link, you can link to any place at ANY TIME. In BoA, Atrus linked back to a time before they were ever there.
Sorry to add to the confusion, but linking to an earlier time doesn't explain the situation in the Book of Atrus. Atrus actually linked to a completely separate, albeit remarkably similar, Age.
Gehn's removeal of the phrases in the Age 37 Descriptive Book forced the Book to choose another Age which still fit the description. The Ages were very similar, but distinct.
[italics in original, bold added]
Based on these writings, it appears to me that Gehn's initial change to Age 37 was realized as a large-scale shift in the local climate. Because nobody had the technology or data to accurately predict said climate, this was an unobserved change and therefore did not break the link. But simply negating the change was not an unobserved modification; Gehn was asking for a world in which the climate shift had never occurred. To do this without breaking the link, Gehn would have had to carefully write in a second climate shift to cancel out the first.