Scientists are able to tell the differences between Flu A, Flu B, Flu C and Flu D. If a vaccine is developed that effectively wipes out 99.99% of Flu Virus A that means that 0.001% of the virus was of a slightly different mutation that is able to withstand the vaccine. When the next year arrives, the Flu Virus A will return but it will be in the mutated form. This can be and has been proved. It can be observed with pure versions of a virus in the lab. This is evolution. Survival of the fittest. It is still Flu Virus A but it has now adapted so that 99.99% is immune to the vaccine. This same thing applies to bacteria that become immune to anti-biotics, mosquitoes that are no longer bothered by repellant and thousands of other plants and animal species that slowly adapt to their surrounding environments. Some live and some die. Those that live make the species stronger at least to certain elements.