Effects that modify the power or toughness of the land creature without setting it will apply to its new base power and toughness no matter when they started to take effect. The same is true for counters that change its power and toughness.

Nissa's Zendikon overwrites any previous effects that set the land creature's power and/or toughness to specific values. Other effects that set these characteristics to specific values that start to apply after the ability resolves will overwrite that part of the effect.

Nissa's Zendikon doesn't remove any abilities the land creature has.