In chapter nineteen of Guns, Germs, and Steel, Jared Diamond posits his researched theory on how Africa became black. He explains that by A.D. 1000 the African continent was populated by five major people groups: blacks, whites, African Pygmies, Khoisan, and Asians. All of them had their own unique physical and language characteristics.
The African Pygmies are different from the black Africans because they are much shorter, have more facial and body hair, and have more reddish skin. Their foreheads, teeth, and eyes are also much more prominent than those of the black Africans.
In terms of language, the Pygmies are the only one of these five people groups who had no unique and particular language; instead, they would assume the language of whatever black tribe they were near. However, when their language was compared directly to the black language of their black neighbors, researchers discovered some distinct words and phrases not used by the black Africans. This, of course, indicates that the African Pygmies had some language and sounds of their own which were absorbed into the language of their neighboring tribes.
Though the African Pygmies were isolated enough to have developed a unique language, their language is now gone.
[D]istributional and linguistic clues combine to suggest that the Pygmy homeland was engulfed by invading black farmers, whose language the remaining Pygmies adopted, leaving only traces of their original languages in some words and sounds.
The cause of the extinction of the African Pygmies' language, then, is that the Pygmy tribes themselves were fragmented and eventually absorbed into the black tribes which surrounded them, and their language was, as you suggest, "abandoned."