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GIM mechanism

I can see how the charge is conserved in the overall diagram but I can not understand how it is conserved at the up to anti-down vertex.

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In your diagrams, time moves to the right. The four vertices that make up the "box" aren't well-ordered in time. So the vertex involving the anti-down is one of the reactions

$$ \bar d u \to W^+ \qquad\text{or}\qquad \bar d \to \bar u W^+ $$

These vertices conserve both electric charge and baryon number.

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