If you go to your local hardwear shop you will find a range of fly killing products - one of these is a pen that you draw on to the place you want to kill the flies & when they land it kills them. Another is a disc you stick - usually onto a window - & contact kills flies.
Alternately you could try spraying the affected areas with a household flea product for treating the house not the animal. These have a similar residual effect lasting 3 to 6 months indoors, but since they are designed to work on fleas I'm not sure if they will work on flies.