If Magmar's Smokescreen Knocks Out the Defending Pokémon, does the new Active have to flip to see if its attack is effective?
No, it only effects the Defending Pokémon the attack was done against.
Source: WotC Chat (2000-02-24)

Relevant cards

Note: All applicable cards may not be listed below.
COL1_60
HGSS1_70
PL3_65