See if you can figure out where they're swarming; that's usually close to the source.
In the interim, you'll need to pull out all your fixtures & clean behind/under them THOROUGHLY - syrup stands, coffee brew area, condiment containers, espresso machine, blender, drain mat areas, etc.
Also make sure that the flies aren't around/inside the pastry case &, if you have a dining area, keep it wiped down - especially soda fountains & icee machines.
Make sure garbage cans are changed out & have working lids.