Did you overprocess the pretzels? Or possibly they needed to be baked longer? This is from Marlen's notes:

Note from Marlen: The pretzels should be about the size of the chocolate chips, not pulverized. You want to taste bits of pretzel as you munch. This is a crunchy cookie. I use a food processor and just pulse until the desired size is achieved.

I would think maybe the pretzels did loose their texture if they sat in the dough overnight...or you made them too small as ginger noted. The pretzels, the nuts, and the large amount of vanilla really make the cookies, IMHO.

I think they are great! You should definitely try again without refrigerating the dough overnight and making sure the pretzel pieces aren't too small.

Good point, Carla. I think you're right that the pretzels probably got soggy in the dough overnight.

Definitely bake the cookie as soon as you make up the dough. The cold is what made the pretzels lose their 'crunch' plus as was suggested-keep them 'chunky'-not ground too fine.

Thanks! The pretzels weren't over crushed so I"ll try again sometime and not refrigerate the dough.