My D7 suffered fold-itis skin rashes. Square Velcro sticky patches in sensitive places worked well. My other bike suffers when I hang the bars on the top tube for storage. Duct Tape (available in a variety of colors) was the answer.

Scratches on folders are inevitable, alas, but of course, you may just be folding it slightly awkwardly.

Why not post a pic of the fold so that The Bearded Ones may pronounce upon any possible folly?