If I flipped heads on Seadra's Agility attack, would that prevent Cradily's Spiral Drain from removing damage counters?
Agility only prevents damage and effects done to Seadra, not other effects that may extend to other Pokémon.
Source: PUI Rules Team (2004-03-25)

Relevant cards

Note: All applicable cards may not be listed below.
COL1_45
HGSS3_28
EXP_12
EX3_40
EX2_3