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In H3PO3 only only 2 hydroxide groups exist, instead of 3. If there is 3 hydroxide group, the phosphorous will have 1 lone pair electrons, which will still satisfy the valence electron of Phosphorous.

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The two isomers you're referring to both exist and are in equilibrium:

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When only one or two protons are removed, resonance stabilizes the anions formed, e.g. the $\ce{HPHO3^-}$ anion:

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The trianion (shown below) doesn't have the benefit of resonance stabilization. This makes removing the third proton much harder.

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