While "Dark Valkyria" is an Effect Monster, you can place Spell Counters onto it with other card effects, like "Pitch-Black Power Stone" and "Apprentice Magician".
If "Dark Valkyria" is treated as an Effect Monster due to the effect of "Superalloy Beast Raptinus" and has a Spell Counter when "Superalloy Beast Raptinus" is removed from the field, the Spell Counter is removed because "Dark Valkyria" is changed to a Normal Monster. If "Dark Valkyria" becomes an Effect Monster again afterwards, its effect can be used once more.