How are whole Haplotypes for Sequencing isolated?
If your aim is to isolate the two haplotypes (chromosomes) maybe you should try flow cytometry. You might read this paper http://www.ncbi.nlm.nih.gov/pubmed/21181533 by Dolezel which is leader in the field, at least for plant chromosomes. I'm pretty sure that the applicability of the method depends on the physical properties of the chromosomes you have (especially their size distribution).