I know that fruit flies have been studied through billions of generations (lasting only several minutes for them), and they are ALL still fruit flies.
Then you know what they were before they mutated into fruit flies ...
Uh, go back to your creationist web-site. You misquoted from them. Of course anyone that had been in biolgy class that week they played with the fruit flies would see that you are seriously in error in your post. But that is ok. We don't really expect you to have even a basic biological background.
Before you can make that statement you need to enumerate the morphological features that make a fruit fly a fruit fly.
In that list of morphological features is there an item that specifies four wings? No there isn't.
In that case can you really make the claim that they were all fruit flies when a number of them had four wings instead of two?
How many morphological changes are necessary before the fly in no longer a fruit fly? Even in the tests that were done, which were not to create new species, a number of mutations produced organisms we would not consider fruit flies.
You are aware I hope that the purpose of the work was not to produce new species but to test the ability of mutations to provide morphological change. To perform this test they had to produce mutations that left morphological changes that were noticeable. To produce noticeable changes the mutations were much more than what would happen in the wild.
Evolution proceeds through the accumulation of changes; an accumulation that is not restricted by any known mechanism.