Cut peaches into quarters and remove pits. Pile peaches into a large, heat-proof bowl.
Bring a kettle of water to a boil. Once it boils, pour the water over the peach quarters. Let them sit for 2-3 minutes, until the skins wrinkle and pull away from the fruit.
Peel the skins away and chop the peaches.
In a large, non-reactive pot, combine the peaches, onion, raisins, vinegar, honey, mustard seeds, ginger, salt, red chili flakes, and lemon zest and juice.
Bring to a boil over high heat and then reduce the heat to medium-high. Cook, stirring regularly, at a brisk simmer for 45 minutes to an hour, until the chutney thickens, darkens, and the flavors start to marry.
While the chutney cooks, prepare a boiling water bath canner and enough jars to hold 4 pints of chutney (I like to use half pint jars for a product like this one).
When the chutney is finished cooking, funnel it into prepared jars, leaving 1/2 inch headspace. Wipe rims, apply lids and rings, and process in a boiling water bath canner for 15 minutes.
When time is up, remove jars from canner and place them on a folded kitchen towel to cool.
Once jars are cool enough to handle, remove rings and test seals. Sealed jars can be stored on the pantry shelf for up to a year. Unsealed jars should be refrigerated and used promptly.