Landauer's principle internals - how it works
You're confused because the example didn't cover all possible cases, and you're extrapolating improperly.

Negation is the operation


  0 &rarr; 1,
    1 &rarr; 0.


This is reversible, and can theoretically be performed using an arbitrarily small amount of energy.

Restore to one is the operation


  0 &rarr; 1,
    1 &rarr; 1.


This is not reversible, and unavoidably  dissipates $k T \ln 2\;$ energy.