Make sure you aren't using the bleach spray on the floors and counters. It doesn't break down sugars and will actually break down the grout on your floors and counters, this allows water to get trapped in the grout and under the tile which is a breeding ground for flies. Next check under fridges for spills and missed inclusions. But that bleach (bathroom cleaner) spray is usually the culprit.

My store fills the drains with a cup of ice, puts the inclusions in the fridge, and puts a clean trash bag over the syrups.

The first one is from my first manager who had worked in food since he was a teenager and he said that it would make the drains too cold for the flies to lay eggs.

The second one sounds super weird but before we did that when we took the trash bag off in the morning we would find a giant swarm of flies.

The third one was suggested by the store manager. (I work in a licensed store, not a corporate one.)

A good way to get rid of the ones you already have - fill a small cup with about half an inch of sugary juice, pull some saran wrap taut over the rim of the cup, roll a small piece of paper into a conical shape, and stab that through the saran wrap. They will fly in, but for some reason, they can't fly back out.

Constant cleaning of the syrup stand, bottles (rinse with hot water and scrub really well with sani rag), rinsing cold bar sink with hot water and making sure the grout in the tiles is scrubbed really well

Clean up ALL syrup and spray the drains with the most toxic thing you can find 3 times a day open/midday/close

We put one towel over each floor drain and spray generously with bleach every night and it keeps the flies out