Say I have a Chandelure with Shadow Tag, while hunting for Moltres (starting with Froakie). Will Moltres able to flee away, or would it be trapped ? And how many times must I encounter Moltres before the last encounter ?
Moltres (or the other two) can not be trapped in battle by any means. You're meant to encounter them 12 times before they remain as stationary pokémon at the Sea Spirit's Den.