The core of something is its innermost part. For example, an apple core . If something is shaken to its core (or to its very core ), it is shaken, or disturbed , in a very deep way, to its innermost essence or soul, if you like.
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NL888 What does "to its core" mean?It's a figurative expression. Think of an apple. "rotten to the core!" (With the apple, it's not figurative.)