1-Toss squash and onions with salt in: Toss squash and onions with salt in a large bowl. Let sit for 1 hour, then drain and rinse well.
2-In a saucepan, combine vinegar, sugar, mustard: In a saucepan, combine vinegar, sugar, mustard seeds, celery seeds, turmeric, and red pepper flakes. Bring to a simmer.
3-Add squash and onions to the pot: Add squash and onions to the pot. Simmer for 5 minutes.
4-Transfer the mixture into clean jars: Transfer the mixture into clean jars. Cool to room temperature, then refrigerate for 24 hours before serving.