I guess your last sentence answers your question. I'm sure some people had found the deleted files, but because that would before the internet was ubiquitous, it was not generally known or recorded.
Or it was recorded, but it was on fidonet or some bbs system that didn't make the transition to the WWW and no one old enough to remember actually remembers or cares anymore.
Yeah, this could well be true. I was using a Hex Editor a lot back in the late 80s and early 90s, and that involved many of the Sierra games. Most of the time I was looking at the files installed on a hard disk though, as I generally installed the game from the floppy to the hard disk first and assumed I had everything. I think it would have been rare for me to be viewing the whole floppy disk of a Sierra game sector by sector in a Hex Viewer, although I did do that a lot for some disks. I'm surprised I didn't spot this back in those days. I bought this version of Space Quest II back in 1989.
My memory of those times was that floppy disks were fragile enough, and software expensive enough, that you would take the original disks out only to install the game (or cough make a backup copy for a friend) and then carefully put them back in the box. So it's not too surprising to me that people weren't studying them closely enough to spot this.
