Repetitive DNA poses distinct challenges to the DNA replication machinery, particularly during the rapid syncytial cell cycles of early Drosophila embryo development. The maternally deposited Blm DNA helicase mediates such challenges that arise during this unique stage of development. Surviving progeny from Blm mutant mothers show a female sex bias, which has been attributed to the absence of the highly repetitive Y chromosome DNA sequences in the developing embryo. If survival to adulthood is dependent on total repetitive DNA content, then Y chromosomes that harbor variable amounts of heterochromatin (a proxy for repetitive DNA content) may show variation in male survivorship. To investigate this possibility, we crossed Y chromosomes isolated from a worldwide sample of Drosophila melanogaster populations into a common genetic background and quantified bulk heterochromatin using a classic position effect variegation assay (“PEV”). After classifying these Y chromosomes as strong or weak suppressors of PEV, we crossed them to Blm homozygous females. Contrary to our prediction, the strongest suppressor of PEV (i.e., the line presumed to have the most bulk heterochromatin, and thus the most Y-linked repetitive DNA) did not exacerbate the female-biased sex ratio among survivors. Indeed, PEV suppression was a poor predictor of progeny sex ratio. However, we discovered one Y chromosome that consistently altered the ratio of female:male survivors compared to all other Y chromosomes tested. Our data implicate the existence of particular Y chromosome features that pose distinct, Blm-dependent challenges to DNA replication. Currently, we are exploring both the identity of these repetitive features and the molecular mechanism underlying Y-dependent replication challenges that arise during syncytial embryonic cycling.