The first thing to note is that chromosomal aberrations are not universally harmful. As William Klug and Michael Cummings point out, there is normally diversity in chromosomal structure within single species:
While the chromosome number is commonly regarded as invariant for a given species, the arrangement of chromosomal material is often polymorphic through chromosomal inversions and translocations. These chromosomal aberrations usually have little direct effect on the phenotype because gene content is rearranged but not altered. (Klug and Cummings 1983:528)
Likewise, chromosome number can change without altering gene content through the fusion or fragmentation of chromosomes. The second edition of Colin Patterson's book Evolution contains a striking pictorial example, showing how the chromosomal patterns of Drosophila pseudoobscura and D. melanogaster can each be derived from the chromosomal pattern of D. subobscura by chromosome fusion: D. pseudoobscura by one fusion, and D. melanogaster by two (Patterson 1999:33).
References:
Klug WS and Cummings MR. 1983. Concepts of Genetics. Columbus: Charles E. Merrill.
Patterson C. 1999. Evolution: Second Edition. London: The Natural History Museum.