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Does a stratagem changing the attack/defence of a character change the base values for the character?

No. For example, if Private Pteraxadon’s Binary Edgewing Scythe upgrade mode removes the base defense from a defending Windblade, Combiner Hunter, it would not remove the +1 from the Camien Toughness stratagem.
Source: Aequitas (2022-08-23)    【Link to Ruling】
Tags: Stratagem