Then the damage is dealt, but protection kicks in and prevents the damage to the Beetle
It gives all creatures you control +1/+1 until end of turn for each experience counter you have, and all your cute little Eldrazi Spawn and Scion tokens will get indestructible and annihilator 1 (whenever a creature with annihilator attacks, the defending player has to sacrifice a number of permanents equal to the annihilator value)
This commander gives your enchantments escape, which is already a very powerful effect
As a hypothetical curve to show quite how obscene this can look, you could cast your copy of The Ringhart Crest on Turn 2, on Turn 3 you use it to resolve Questing Beast, and then you get to land your Yorion on Turn 4, blinking the Crest to turn it into a Kolvori
Indestructible permanents can be a real hassle, especially when it's something like a Darksteel Forge or an Eldrazi Monument that just causes headaches for everyone