Genomic scans should be slightly more reliable. This is based on Van Raden et. al. J. Dairy Sci. 94 :5673–5682: "...rates of increase in genomic and pedigree inbreeding per generation should be slightly reduced with genomic selection ..." Also, from the same paper: "Pedigree relationship matrices ignore common ancestry shared by base animals within breed and may not approximate genomic relationships well in multibreed populations."

Pedigree information ignore Mendelian segregation term to calculate genetic relationship coefficient and consider only IBD alleles and also it supposes base population are unrelated and not inbred, whereas allelic relationship is based on genotype arise  from SNP information, includes IBD and IBS alleles even in base population, therefore total homozigosity and average allelic idendity can be used in inbreeding coefficient calculation.thus genomic scan is much more reliable than pedigree information and rate of increasing in inbreeding reduces per generation.