Preheat oven to 425º F . Line two large sheet pans with parchment paper.
Heat a large skillet over medium heat and cook the bacon until the fat begins to render, approximately 6 minutes. Add the onion and cook until they begin to soften, approximately 5 minutes. Remove from heat and set aside to cool slightly.
Add the goat cheese, half & half, sour cream, egg yolk and thyme to a blender and pulse to combine.
Lightly flour your surface with flour. Add a sheet of puff pastry then dust the top with flour and roll out to approximately 10"x12" rectangle.
Use a fork to dock the puff pastry with the exception of a 1-inch border. Repeat with the second puff pastry sheet.
Divide the custard mixture and spread it over the docked area of each puff pastry sheet. Then top each with half of the bacon/onion mixture.
Bake the tarts for 20 minutes then sprinkle with the gruyere cheese and bake an additional 3 - 5 minutes, until pastry is golden and cheese is melted.
Remove from oven and garnish with chives. Cut and serve.