I have two fly genomes from a species for which there are no other genomes available. One genome has been assembled from PacBio reads (N50=~400,000bp) and one from 10X (N50=~250,000bp). The genome is about 250-300Gb long.
I would like to use the scaffolds from both these genomes to create an assembly with longer scaffolds.
I would imagine that you need to look outside the 'classic" field of high throughput sequencing. You most likely need a long read assembler that works off end-overlaps rather than the de Bruijn graph type of assemblers.
For example this (I found this as a search so I can't comment on its applicability)
Maybe you have already done this, I'd align the two genomes first to see a synteny map. And depending on what you see, I'd plan the assembly. For the alignment Mummer (http://mummer.sourceforge.net/) may help, or another tool.