Scenario:
I play Timber Protector which makes all other Treefolk indestructible (I only have Treefolk in play).
My opponent plays a Day of Judgment.
Does this only destroy the not-indestructible Timber Protector?
or
Does Timber Protector get destroyed, all my Treefolk lose their indestructibility, and then they get killed at the same time?
The destruction only happens once, it's instantaneous, and there's only one creature vulnerable to it when it happens.
610.1. A one-shot effect does something just once and doesn’t have a duration. Examples include dealing damage, destroying a permanent, putting a token onto the battlefield, and moving an object from one zone to another.
Think of it a state machine. There's only two game states in the scenario.
700.4. If a permanent is indestructible, rules and effects can’t destroy it. (See rule 701.6, “Destroy.”) Such permanents are not destroyed by lethal damage, and they ignore the lethal-damage state-based action (see rule 704.5g). Rules or effects may cause an indestructible permanent to be sacrificed, put into a graveyard, or exiled.
Therefore, as ikegami said above, all treefolk are indestructible when the Day of Judgement resolves except for the Timber Protector and survive, while the Timber Protector is destroyed and goes to the graveyard.
Now, if another board wipe occurs before you give them indestructibly or regeneration, then all of your treefolk are destroyed.
EDIT:
However, if you were to use a board sweeper such as Blasphemous Act instead all your creatures would be destroyed because then all creatures would have 13 damage marked on them, the Timber Protector would be destroyed because of damage, then all other treefolk would lose indestructibility and die because of lethal damage (which wouldn't leave the creature until the cleanup step).
