I have never had any luck writing Apple II floppys back to original disks with the KF either, but that is something I need to re-investigate. I believe the main problem is simply that the KF does not "splice" tracks that are not index aligned (Apple 5.25" drives have no index sensor), nor does it try to re-align the tracks. There is also the problem that if you are using a 1.2mb floppy drive to write the disks, the disk must be degaussed first (PCs have the same problem reading 360k disks written in 1.2m drives with genuine 360k drives). Some PC 360k drives seem to have some issue with GCR and the Kryoflux forces you to use a 1.2mb drive when decoding images anyway.
Unfortunately, the kryoflux was designed as a "preservation" tool, so use as an interoperability tool takes a backseat.
In the mean time, there is a software tool called Apple Disk Transfer ProDOS (ADTPro) that you can use to connect an Apple II to a newer PC via a serial port and transfer disks that way. It even bootstraps itself via serial, so no existing Apple II software is needed.