Flip Effects are Triggered Effects, so if a player flipped a flip effect monster, the effect will trigger as chain link 1. Fiendish Chain can be chained to it, to negate the effect when it tries to resolve.
However, if the monster is flipped by an attack, then the trigger happens during the Damage Step. There are restrictions against what you are allowed to activate during the damage step, and Fiendish Chain can't be used here. So it could not stop a Flip Effect at that time.
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The Flip Effect itself is a Trigger, an activation of a monster effect. Herald of Perfection cannot negate the summon itself, but can chain to and negate the actual Flip Effect trigger.
You cannot use Royal Command to negate and monster whose effect activates when it is flip summoned, as Royal Command only activates for FLIP: monsters.
No. A monster that is face down does not 'flip' when destroyed by a card effect, and will not trigger any flip effects.
No, but it does stop it. 'Negate' is a very specific game term, which has other meanings and significance. All Sakuretsu Armor does is make it impossible to continue the attack step by removing the attacking monster - the Damage Step will not be entered, so the defender will not flip if face-down, and no damage will be calculated. However it is still not accurate to say it 'negated' the attack, which other cards like Necro Gardna actually do.
Flip effects will activate if flipped manually by Flip Summon, or when attacked. Also must include "FLIP" in all caps for its effect to activate, or say 'when this card is turned face-up'. For example if a monster such as Guardian Sphinx is flipped face up by an attack or an effect (spell, trap or monster), the effect does not activate, because only a Flip Summon triggers it, not a generic flip. When a card effect destroys a face-down monster, the monster is destroyed and flip effect isn't activated because the monster never flips. Mystic Swordsman Lvl. 4 destroys the monster it attacks without flipping it, so a Flip Effect monster attacked by it will not get its flip effect. To summarize, if a FLIP effect monster is attacked while face down, then it will activate. But if it's destroyed by a card effect while face down then it won't activate. Some card effects let you flip monsters face up and let the flip effect activate, like book of taiyou. But others, like ceasefire don't let it activate. If it says 'when this card is flipped face up' then you have to do that manually on your own turn.