If an effect prevents Sinistcha ex's "Re-Brew" attack from placing damage counters onto the target Pokemon, do I still shuffle the Basic {G} Energy cards into my deck?
No, if you don't place any damage counters, you don't shuffle the Energy into your deck.
Source: Twilight Masquerade FAQ; TPCi Rules Team (2024-05-23); TPCi Rules Team (2024-07-25)

Relevant cards

Note: All applicable cards may not be listed below.
SV6_23
SV6_23