Question

Does protective mycelium protect from damage done?

Comments

Not a full answer, but https://bulbapedia.bulbagarden.net/wiki/Toedscruel_ex_(Obsidian_Flames_22)

Answer 1

Prevent all effects of attacks used by your opponent's Pokémon done to all of your Pokémon that have Energy attached. (Existing effects are not removed. Damage is not an effect.)

source
I believe this means the ability does not prevent direct damage.

Comments

Direct if they have energies attached

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The description says it prevents effects if they have energy attached, and doesn't count damage as an effect. So either way the damage should still happen.