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If my opponent has one face up Secret Action and two face down Secret Actions, do I do 1 damage to each enemy, or 3?

You would do 1 damage to each enemy, then 1 damage again, and then finally 1 damage again. The 'or' in "face up or face down" should be read as 'and/or', and the damage is one at a time rather than all at once.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Decipher
If I have one face up Secret Action and one face down Secret Action, do I get +2 attack or +4 attack?

You get +4 attack. The 'or' in "face up or face down" should be read as 'and/or'.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Decepticon Pounce, Infiltrator
If I have Secret Actions in my hand, scrap pile, under a character, or even in my KO area (say because of Daring Escape), do those count?

No. Pounce counts only the Secret Actions in your played area.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Decepticon Pounce, Infiltrator
If I play Swarm! and flip a card with no battle icon, will Skywarp get +3/+3 in bot mode?

Yes.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Skywarp, Teleporting Seeker
When Chromedome flips to body mode and you get to KO an opponent's Action, does that trigger Decepticon Shockwave's bot mode?

No. The Action is 'put' into the KO area, not scrapped, thus it does not trigger Decepticon Shockwave's bot mode.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Chromedome, Computer Programmer
Which mode do Trypticon and Metroplex minions start in?

By default all characters start in the mode showing their star cost. So the minions, while not visible under Trypticon and Metroplex are in alt mode. Note that while Relentless Invasion card does provide a way for a Trypticon minion to be under Trypticon in bot mode, it will be deployed in Alt mode (per WotC FAQ).
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Metroplex, Autobot City
If you attack with Nightbird and use her bounty ability, can you use steamroll from the opponent's scrap pile?

You can play the Steamroll, however you cannot use it for Nightbird's attack as by the time Steamroll is played, Nightbird's damage was already applied and the defender was already KO'd. If you happen to attack again on that same turn, Steamroll could be usefully applied to an attacker.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Nightbird, Enigmatic Agent
If Hold the Line heals a character to 0 damage while Barrage is attacking, does Barrage still get Bold 2?

No. The Hold the Line is revealed and repairs when the defending character 'defends' (1.3.1.5 of the Expanded Rules), whereas the Bold value isn't locked in until later when the Bold and Tough are calculated (1.3.2.2 of the Expanded Rules).
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: Barrage, Merciless Insecticon
If a War of Attrition is used to KO a character with a Head, can any additional War of Attritions be used on the Head?

No. The KO trigger on the character with the Head has to wait until any subsequent War of Attritions have been played.
Source: Aequitas (2021-06-03)    【Link to Ruling】
Tags: War of Attrition