Omega−3 is a sensitive nutrient, susceptible to damage from light and air. Seeds that are being used as a source of Omega−3 should ideally be kept whole until needed, or otherwise kept in a dark, sealed container, preferably in a refrigerator, and used within a month.
Omega−3 can also be damaged by heat, particularly the high heats of frying. The heats involved in baking, however, should be fine.