Line a baking sheet with parchment paper.
Microwave the flour in a small microwave-safe bowl for 1 minute. Remove and stir well. Microwave for an additional minute or until the temperature reaches 180 degrees F. Sift into a medium bowl, then whisk in the baking soda and salt. Set aside (see Cook's Note).
Beat the brown sugar, granulated sugar, butter, yogurt and vanilla with an electric mixer on medium-high speed in a large bowl until well combined, about 2 minutes. Add the flour mixture, and mix on low speed until well incorporated. (Turn off the mixer and use your hands to help combine if needed.) Fold in 1/3 cup of the chocolate chips with a rubber spatula, or mix them in with your hands.
Scoop tablespoonfuls of the batter, and roll them into smooth balls. Put them on the prepared baking sheet, and refrigerate until chilled, about 1 hour.
Melt the remaining 2/3 cup chocolate chips and the shortening in a medium microwave-safe bowl in the microwave in 30-second increments, stirring in between, until the coating is smooth and thin. Drop the chilled balls into the coating, and roll them around with a fork to fully coat. Remove each truffle with the fork, letting any excess coating drip off, and return to the baking sheet. (If the coating begins to harden, microwave it for a few seconds to warm it up and thin it out.) Refrigerate the truffles until the coating is completely set, about 1 hour. (The truffles can be refrigerated in an airtight container for up to 5 days.)
Microwaving the flour to 180 degrees F may reduce the risk of foodborne illness associated with eating it raw or undercooked.
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