Well, here comes the problem. Almost all original disks carry some kind of copy protection. If there was no copy protection, we could preserve stuff just by creating disk images or refreshed originals using a simple sector copier. As far as I understand Kryoflux is used to preserve stuff that is difficult to being preserved by normal means.
But what is preservation good for if things cannot be retrieved? That's like creating uncrecoverable backups.
Okay, thanks for the information, that DTC cannot write back raw stream files from non-index-aligned disks. Though I do not understand why that is so. I guess there will be some note in the stream file where the index pulse occured and what is so difficult about writing the following bits until the next pulse back to disk.
People were able to create highly advanced protetion schemes even with a Floppy Disk Controller Chip being involved. There were upgrades to drives which were capable to bypass the FDC to read and write plain bits from or to the tracks. This sounds a bit like how Kryoflux works. And Kryoflux has the advantage of some 30 years of evolution in computer technique...
If we create disk images from the stream files and write those back creating index aligned disk that disk has nothing to do with the original, has it? That is a black and white photocopy of a Picasso painting.