If I used Sandaconda's "Coil" attack and my opponent retreats their Active Pokemon, do I still do an extra 120 damage to the new Defending Pokemon?
Yes. The attack states "your opponent's Active Pokemon". That is referencing any Pokemon that is in their Active Spot.
Source: Sword & Shield FAQ (2020-01-24), TPCi Rules Team (2020-02-06)

Relevant cards

Note: All applicable cards may not be listed below.
SWSH1_109
SWSH1_109