Yes, some of these repeats (~ hundreds of kb) can be resolved with very long Nanopore reads. To separate homologous chromosome for diploid is indeed a related but not 100% identical problem. FALCON-Unzip and other diploid phasing approach makes strong assumption to separate the reads/variations into two piles. In more general repeat cases or polyploid cases, that assumption need to be relaxed and may create different kind of graph puzzles.