Combine onion, squash, apple juice, vinegar, garlic, salt, pepper, mustard and red pepper flakes in a large pot. Bring to a simmer. Slowly add pectin. Bring to a boil and add butter. Bring to a rolling boil that you cannot stir down
Add honey and sugar. Return to boil for 1 minute, stirring constantly. Ladle into jars. Refrigerate for 2–3 months or process for canning.