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"The recent discovery of a red oak tree sap that is anticipated to advance experimentation with natural substances in order to create cancer medicines will be able to provide chemists with a more potent mixture to work from than other trees and at a lower cost."
In here, "that" refers to "the recent discovery", and if instead we had "which" it would refer still to "the recent discovery".

"Fossils of a whale that beached on an African shore more than a million years ago and was subsequently
butchered by hominids have been recovered by paleontologists."
Here, "that" refers to the "whale" and not to "fossils".

Why on the 1st example "that" refers to the first noun and on the 2nd example to the second noun?
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Pedro121212
"The recent discovery of a red oak tree sap that is anticipated to advance experimentation with natural substances in order to create cancer medicines will be able to provide chemists with a more potent mixture to work from than other trees and at a lower cost."
In here, "that" refers to "the recent discovery", and if instead we had "which" it would refer still to "the recent discovery".

"Fossils of a whale that beached on an African shore more than a million years ago and was subsequently
butchered by hominids have been recovered by paleontologists."
Here, "that" refers to the "whale" and not to "fossils".

Why on the 1st example "that" refers to the first noun and on the 2nd example to the second noun?
that has significant flexibility in terms of what it can modify, based on what makes sense.

In your first example, recent discovery is anticipated to advance experimentation, while in your second example, whale beached on an African shore. In other words, in the context of the intended meaning of the sentence, recent discovery and whale make sense to be modified by that.

Another official example below, in which that modifies the faraway noun historical account, because this is what makes sense.

Written in ink or engraved by stylus, more than 2,000 letters and documents on wooden tablets excavated at the site of the old roman fort at Vindolanda in northern England are yielding a historical account of the military garrison in the first and second centuries that is as vivid in its details of personal life as that gathered from Pompeii.

On the other hand, which generally does not show this kind of extreme flexibility.

p.s. Our book EducationAisle Sentence Correction Nirvana discusses the issue of which vs that, its application and examples in significant detail. If you or someone is interested, PM me your email-id; I can mail the corresponding section.