I never heard of files getting deleted when blacklisted…
Anyway, if files are really vanishing the following is a pretty obvious workaround but maybe it will make your life easier until you get official support from devs:
Install kernel 4.x.y.z tar cfz /somewhere/4.x.y.z-drm.tgz /lib/modules/4.x.y.z/kernel/drivers/gpu/drm /boot/your-4.x.y.z-initrd.img
Then if you decide you need to restore just do
# tar xf /somewhre/4.x.y.z-drm.tgz -C /
# depmod 4.x.y.z