From a Doctor I know.

"It can be clinically difficult to distinguish between the two illnesses. The prior tests have simply detected the Covid 19 virus. If the person had influenza, the test just came back negative for Covid. It did not return as a positive for Covid-19 when the patient had influenza. The newer tests have testing for Covid-19, Influenza A and Influenza B all in one test. This is simply saying to switch to the combination so that if the patient has any of the 3, it will tell us which. We have already been using the newer tests."