Place blueberries in 4 quart saucepan; add onion, vinegar, raisins, brown sugar, mustard seed, ginger, cinnamon, salt, nutmeg and red pepper flakes.
Bring mixture to a boil; simmer over medium heat, stirring occasionally, for about 45 minutes, or until chutney is thick.
Meanwhile, wash 4 half pint jars. Keep hot until needed. Prepare lids as manufacturer directs. Ladle the hot chutney into 1 hot jar at a time, leaving 1/2 inch head space. Wipe jar rim with a clean, damp cloth. Attach lid. Fill and close remaining jars. Process in a boiling water bath for 15 minutes (20 minutes 1,001 to 3,000 feet; 25 minutes 3,001 to 6,000 feet; 30 minutes above 6,000 feet)
Notes: Try this chutney with roasted turkey, duck or goose, meat or curries. Mixed with mayonnaise or plain yogurt it makes a piquant dressing for salads made with meat, poulty and fruits.