I have 30 NILs samples of Drosophila that were, first, selected for a certain morphological trait and then isogenized. I started with an F1 between two species (A and B) and followed by backcrossing females with males of species B and selected lines showing the phenotype of species A for the trait of interest. Since I have the genomes of both parents. What is better than GBS (reduced genome) or skim secquencing?
Have a look at this paper. I think skim sequencing (usually called skimGBS) will provide more markers at a lower cost per marker, but it will cost more per sample.
But I am not sure either method is the ideal for NIL lines. After a few rounds of introgression (how many did you perform), most of the genome should already be from species B. Do you have an idea of the trait architecture? How many genes or regions are involved? Some preliminary mapping information? For example, if you already know the region of interest, you could map by amplicon sequencing.