Place work order without delay for pest removal. Figure where the food source for the flies are coming from, then clean the area well. Sounds like some syrup had spilled in unseen spot.
Hey red, needs some help here.
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.
Yes clean and put in a work order. But there is another thing you can do in the interim, my health department told me this, fill a salt shaker (like the powders are in at SBUX) with apple cider vinegar. It will attract the flies and they'll go into the vinegar and die.