1. The book was discovered in a used bookstore in Chicago.

2. The book was discovered in a secondhand bookstore in Chicago.

3. I found a rare book at a used bookstore.

4. I found a rare book at a secondhand bookstore.
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In each sentence, can we use both 'secondhand' and'used'?

Yes, you can. When referring to a book store, "used" is more common, I think, but "secondhand" is appropriate.