My friend reported the break-in to the police as soon as they discovered what had happened.
Can I replace ‘discovered’ by ‘uncovered’?
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They have different inferences.
"Discovered" tends to be used for things which you have learned about for the first time, for example:
I just discovered a great new TV show.
You may have only just discovered it, but it wasn't "hidden".
On the other hand, "uncovered" suggests that somebody else covered it up. It tends to mean that you found something which was meant to be a secret.
In your example, the crime was not particularly clandestine. The people that broke in must have known your friend would come home and find the property in the state they left it. If they did nothing to cover it up, nobody really "uncovered" anything. I do not think "uncovered" is appropriate in this example.
Yes, they are synonymous in this case. That said, there's rarely such a thing true synonymity. The words generally mean the same thing, but can convey subtle differences and undertones.
In your example, "uncovered" suggests that they found the specific thing they were looking for (like opening the fridge to find something to eat). "Discovered", on the other hand, suggests that they just came across it, perhaps with intent to find something, but not knowing exactly what (like a scientist on an archeology dig).