[note: I thought the OP said "proton"]

Best case? atoms shrink slightly and some changes to how chemistry works

Realistic case? The change in nuclear binding energies renders protons unstable, making many elements unstable or radioactive. All matter suddenly becomes much heavier, changing gravity and internal pressure, which in turn disrupts stellar and planetary structures. Fusion reactions depend on precise mass differences between particles, which may alter how stars generate energy, or completely prevent them from forming altogether. Additionally, since proton mass is tied to the strong nuclear force, it will fundamentally alter physics, and it's likely that protons will decay into neutrons, preventing atoms from existing at all.

The first wish would affect how fluids act under pressure, including how our blood would move throughout our bodies. Depending on the exact effects, the wisher may not even get the chance to make the second wish because their blood would either stop moving, or they would drop to ground as every capillary in their body ruptures causing an immediate loss of blood pressure, quickly followed by loss of consciousness and then death.

IF they live long enough to make the second wish, then they probably wouldn't live long enough to make the third.