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Can other effects change the amount of damage done after Pierce is applied?

Yes. For example, say a character with Pierce 4 attacks Insecticon Skrapnel in bot mode. (He has the ability "This can't take more than 3 attack damage from a single attack.") After battle cards are flipped, the attacking character would do 2 damage, but Pierce raises that to 4. Insecticon Skrapnel’s ability would then reduce the damage done to 3.
Source: Wizards of the Coast (2018-10-11)    【Link to Ruling】
Tags: Pierce