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Did you read the whole article? What about the calls from the program itself which check that you are running the modified DOS? Might you be confusing this with

• applehack1234 11y ago
  I was running the modified DOS. Initially I booted the Math Blaster disk and ran from there. Later I realized I could boot normal DOS, and then swap the DOS in memory. I don't recall if I had to mess with zero page. I think those calls did it automatically, but I don't remember. This also explains why the BASIC programs were obfuscated. Once you find the calls to switch the RWTS, the rest is easy. Getting around the obfuscation wasn't too hard though. I just ran the program and then interrupted it. I do suspect that I had a different version. The directory listing looks a bit different, and I don't recall so many control characters in the filenames. It's possible that they published an updated version with more obfuscation (although it's also possible that I've just forgotten after so many years). As as aside, I wasn't primarily interested in reverse-engineering the copy protection when I did this. I was more interested in their graphics drivers. The program had a thing where it would override the standard functions for drawing characters to the screen, so you could use the standard PRINT command and instead of using text mode, it would draw bitmapped characters into the graphics page. I thought it was rather clever.