Well, in my case (back then, anyhow) was that all of my source files were in DMS format. I had no intention of un-dms'ing the files to actual disks. For one, it's terribly slow. For another, DMS does not report that it is writing to bad disk sectors, it just does its thing. Both of these issues were resolved by unpacking to a virtual (FMS) disk. Then, after unpacking, the adf is there and you only need to copy it (or in my case, I used DOpus Copy As to the actual game name and disk number.)
For the most part, this was a productive process. It's just that somewhere along the ways, those virtual disks expanded. And I don't understand what caused this to happen. It could be FMS, or some other process that caused them to elongate. As long as you made a point to look at the filesize every time, there was no issue. But when converting literally hundreds of files, the eyes grow weary, the process becomes systematic and a few slip through the cracks.