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Does transforming a Car-mode character in the KO pile activate Cliffjumper's alternate mode ability?

Not unless specifically stated. K.O.’d characters flipping wont trigger any abilities unless otherwise stated.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: KO, Play
Am I allowed to count the cards remaining in my deck (Obviously without looking at them face up)? Am I allowed to look through my scrap pile at any time, or only when prompted from a card? (e.g. Wheeljack or Jetfire)

Yes and yes.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Play
When I play Cornered! and force my opponent to flip one of their character's do they get to use a "when you flip to this mode” Ability on my turn?

Yes. If you play Cornered! on an opponent’s character, they get to use a flip ability on that turn.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags:
Can Rapid Conversion be used to flip a character in the KO area? We know now that we can use our flip for the turn to do this, can cards like Rapid Conversion be used?
No, cards cannot effect cards in the K.O. Area unless specifically stated.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Rapid Conversion, Rapid Conversion
Would Thrust grant +5 to Optimus Prime - Battlefield Legend if Rapid Conversion was played when using Prime’s bot mode ability.

No. The amount of bonus granted by Thrust is granted at the time his ability is triggered and not modified afterwards.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Thrust, Supersonic Interceptor
Common Megatron is in Bot mode. He has Grenade Launcher equipped giving him +4 attack. He attacks Barrage in Bot mode. Megatron does not flip any orange icons and Barrage does not flip any blue icons. Megatron's attack is 8 w/Pierce 3 (due to his ability), while Barrage has 2 defense. Does he only deal 6 damage for the entire attack or 3 only due to his Pierce 3?
6. Pierce is a minimum damage.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Megatron, Decepticon Leader, Pierce
Arcee is in Bot mode. She attacks Barrage in Bot mode. Arcee flips 3 orange icons and Barrage flips 2 blue icons. Arcee's attack is 4 w/Pierce 4 (due to her ability), while Barrage has 4 defense. Does she only deal 0 damage for the entire attack or 4 only due to her Pierce 4?
After flipping the three orange, she has Pierce 4, meaning she would do a minimum of 4 damage.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Arcee, Skilled Fighter, Pierce
Arcee is in Bot mode. She attacks Barrage in Bot mode. Arcee does not flip any orange icons and Barrage flips 2 blue icons. Arcee's attack is 1 w/Pierce 1 (due to her ability), while Barrage has 4 defense. Does she only deal 0 damage for the entire attack or 1 only due to her Pierce 1?
In this scenario, Arcee deals 1 damage.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Arcee, Skilled Fighter, Pierce
While playing Chromia, you trigger her ability by flipping 2 white icons for your first 2 battle card flips, is that when your draw into hand happens? Or do you continue your battle flips then take your draw into hand?

Resolve all of the flips and then draw into your hand.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Chromia, Special Ops
Optimus Prime - Battlefield Legend flips Supercharge, would this result in additional Bold 3 if I played that from his ability?
He would have Bold 3, but would not be allowed to flip additional cards.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Optimus Prime, Battlefield Legend, Optimus Prime, Battlefield Legend
If Optimus Prime - Battlefield Legend attacks in Bot Mode and you flip a New Designs, can it be used to put an upgrade on to one of my characters? Also is this the same if I flip a Brainstorm?

Yes to both!
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Optimus Prime, Battlefield Legend, Optimus Prime, Battlefield Legend
Force Field states "if the upgraded character would take 5 or more attack damage - instead scrap this card and the upgraded character takes 4 attack damage." What happens when the target received 4 or fewer attack damage? Do they take that damage and keep Force Field equipped until 5 attack damage is received or does it still get scrapped even if you have only taken 3 attack damage?

Force Field will not be scrapped if you take 4 or fewer attack damage on one attack, and it does not remember previous attacks, even in the same turn.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Force Field, Force Field
What happens if I have Megatron - Living Weapon equipped with 2 weapons and an armor and I play Swap Parts?

In this scenario, if the other character you are choosing with Swap Parts does not have an ability or effect that allows them to hold multiple weapons, you will be able to bring the armor and a weapon of your choice to them. The remaining weapon will stay on Megatron.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Swap Parts
If I am playing Autobot Mirage in his Bot Mode and I hit three white pips while attacking, he untaps. Does this mean I get an additional attack this turn or is he just untapped for next turn? The only reason I ask is because his effect states "during his first attack" so I felt it implied he could attack more than once that turn.

Ordinarily, he would only get one attack and then untap. However, if your opponent is completely tapped out, Mirage and any of your other untapped characters will get an additional attack.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Autobot Mirage, Lone Wolf
Have y'all clarified as of yet if the new Grimlock can fetch the Wave 1 Dinobots?

Yes. As written, Grimlock - Powerful Commander can find Wave 1 Dinobots.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Grimlock, Powerful Commander
Are Combiners able to flip to their separate alt modes once they are combined?

Currently there is no way to flip a Combiner once it is combined.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Combiner
Does Motormaster take the damage with his Alt Mode effect?

Motormaster takes damage that would normally be dealt to him, but does not take damage meant for other characters.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Motormaster, Stunticon Leader
Can a character in the KO area be flipped, when you choose a character to flip for the turn and/or through action cards like Rapid Conversion?

You can flip for the turn, but no cards in the game can effect characters in the K.O. Area unless specifically stated.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: KO
If a character flips in the KO area, will you benefit from any "When this character flips to this mode -" abilities? Do flip abilities matter if they're on the field or in the KO area, as long as the action of flipping happens?

K.O.’d characters flip abilities do not trigger when flipped unless specifically stated.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: KO
If I'm attacking with Nemesis Prime and in the course of my attack burn through my deck, his ability triggers and I shuffle. Once done shuffling, the bottom card goes under him. Does he instantly get the +3 attack, or does it get added to his next attack?

He gets the +3 attack instantly.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Nemesis Prime, Dark Clone, Nemesis Prime, Dark Clone
Can Grimlock - Powerful Commander put another Grimlock - Powerful Commander into the KO area?
Yes.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Grimlock, Powerful Commander
Must I attack every turn?

You must attack if you are able.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Play
Must I flip a character every turn?

No. It’s your choice whether or not to flip a character.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Play
Does Nemesis Prime keep his attack power from recycling scrap when he transforms to truck mode?

The ability that grants the attack bonus is not on his truck mode, so it does not increase his attack, although the face-down cards remain under him.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Nemesis Prime, Dark Clone, Nemesis Prime, Dark Clone
The rulebook says "When your turn ends, put all battle cards you flipped for attacks during that turn into your scrap pile. Also put any Actions you played that turn into your scrap pile." When do you scrap the cards the defender flipped for attacks?

At the same time.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Play