If I use Baxcalibur's "Super Cold" Ability while my opponent has Gengar ex with "Gnawing Curse" in play, do I put 2 damage counters for each Energy card attached from "Super Cold"?
Yes, you do.
Source: Temporal Forces FAQ; TPCi Rules Team (2024-03-21)

Relevant cards

Note: All applicable cards may not be listed below.
SV5_104
SV5_104
SV2_60
SV2_60