Which is exactly the point. The individual lines could interbreed quite happily. The fact that not even sterile offspring of attempted crossbreeds occurred proved that those two lines of fruit flies are less closely related than (for instance) tigers and lions, or horses and jackasses. The fact that they still looked like fruit flies is irrelevant to the scientific point proved.
"Also since this was done in a lab where intelligent design was super-imposed this would in fact invalidate the very idea that it is a natural process proving macro-evolution."
Yes, but the mechanisms were the same as the ones that act in nature, so it was an ideal laboratory proof of "macro" evolution.
You need to re-examine the results. The mutated flies were completely incapable of re-producing.