it depends on the flipping condition:
"Skill Drain" will negate Flip Effects, and you can chain the activation of "Skill Drain" to the activation of a Flip Effect, but you cannot activate "Skill Drain" in the Damage Step because it does not specifically modify ATK or DEF, so you cannot chain "Skill Drain" to a Flip Effect that is activated because a monster was attacked while face-down.
Official rule from Netrep.net
I hope this helped you