Final answer:
Homologous chromosomes have identical genes, but the alleles for these genes can vary as they come from different parents. Recombination during meiosis shuffles these alleles, increasing genetic diversity without altering gene order. The recombination process itself is the exception where gene order remains unchanged.
Step-by-step explanation:
Homologous chromosomes carry the same genes in the same linear order, but the specific alleles may vary between the two chromosomes. These differences in alleles contribute to the genetic diversity within a species. Despite having the same genes, each homolog comes from a different parent, hence alleles for each gene location, or locus, can differ. This variation is essential for the process of recombination, or crossover, that occurs during the first division of meiosis. Recombination allows maternal and paternal alleles to combine onto the same chromosome without changing the gene order, leading to a shuffled assortment of alleles across the chromosome.
The exception noted in the question is likely referring to the recombination process itself. While it is true that homologous chromosomes exchange segments of genetic material during meiosis, the actual gene order remains unchanged. The exchange only involves the alleles, creating new combinations of traits on each chromosome.