Pulse ½ cup pretzel twists in food processor until only fine sandy-like pieces remain. Or fill up a plastic bag and smash with a rolling pin or wine bottle until fine to make ¼ cup pretzel flour. Chop ¾ cup pretzels and leave the remaining ¼ cup pretzel twists whole.
In a medium bowl whisk all purpose flour, pretzel flour, baking soda and salt to combine.
Cream butter, sugar and brown sugar until light and fluffy. Then add eggs, one at a time until smooth before stirring in vanilla.
Gradually add flour mixture and stir just until combined. Add chopped pretzels and chocolate chips. Stir. Scoop by rounded teaspoons onto ungreased baking sheet. Add a whole pretzel or a few large pieces to the top of each cookie and sprinkle on a few chocolate chips.
Bake 4 minutes in preheated oven, remove and smooth the chocolate chips into a smear over the top. Sprinkle fleur de sel and continue baking just until beginning to set in the center 2-3 minutes more. Remove and let cool on baking sheet 1 minute before transferring to racks to cool. Keep in airtight container at room temperature for up 5 days or freeze up to 3 months.