User blog comment:B214/Volume 22 spoilers/@comment-95.90.227.74-20161018202609/@comment-29963364-20161019044958

They used the Holy Grail to study Issei's remaines (which possessed some of Ddraig's aura due to being the possessor of the Boosted Gear), thereby using that info to create as close a copy of the Boosted Gear as possible.

Yes Issei's flesh was used in the creation process, but only as a blue-print, not an actual building material. It's not like the Scale Mail Replicas each have pieces of Issei's flesh, or that they have clones of Issei inside them. They're just empty suits of armor.