Stir the squash cubes, broth, thyme, nutmeg, and salt in an Instant Pot. Lock the lid onto the pot.
Option 1Max Pressure Cooker Press Pressure cook on Max pressure for 4 minutes with the Keep Warm setting off.
Option 2 All Pressure Cookers Press Soup/Broth, Pressure Cook or Manual on High pressure for 5 minutes with the Keep Warm setting off. The valve must be closed.
Use the quick-release method to bring the pot’s pressure back to normal. Unlatch the lid and open the pot. Stir in the milk and cream.
Use an immersion blender to puree the soup right in the pot. Or work in halves (or even thirds) to puree the soup in a covered blender. (Remove the knob from the blender’s lid and place a towel over the opening so that pressure cannot build up and spew hot soup onto you.) If necessary, return all the soup to the cooker.
Press the SAUTÉ button and set it for LOW, LESS, or CUSTOM 250°F. Set the timer for 5 minutes .
Bring the soup to a simmer, stirring often. Meanwhile, put the butter in a small, microwave-safe bowl or measuring container and melt it in 5-second increments on high in a microwave. Use a fork to stir in the flour to make a thin paste.
When the soup is simmering, whisk (do not stir) the butter mixture into the pot. Continue whisking until the soup is slightly thickened, about 1 minute. Turn off the SAUTÉ function and cool for a couple of minutes before serving.