What MANUALS are you talking about? Please be more specific. What you call a manual is probably what I called "hint sheets". Given I worked there, I viewed them differently.
Basically in the earliest days of the company (from 1987 onwards), when someone would buy a game from Apogee, we would send out floppy discs along with a "hint sheet" which contained some hints and tips. These hint sheets were nothing more than single pieces of paper. Had tips, cheat codes sometimes, things like that.
Wolfenstein 3D was the first game I can think of with a proper full on "game manual". The next few games after that were the old way - floppies with hint sheets. After that, I believe the next game to have a proper full on manual was I think Duke Nukem II in December 1993. Also, Blake Stone, as both it and Duke Nukem II were released the same day.
Without going down the complete list of games, I forget what game was the final one with one of the old style hint sheets. I'm thinking it was Bio Menace, but I'm not entirely sure.
From that point onwards we produced print manuals for everything we released. Some of them were squares that fit inside CD jewel cases (Duke Nukem 3D was like that), but most were the "longer rectangle" types.
In 2009 when the company was close to closing, I went and scanned EVERYTHING in as a pdf. Both the hint sheets and the manuals. In the last two days I was at the "old" 3D Realms, I repackaged everything in a DOSBox, digital format so the games could continue to be sold through a digital store that we launched at that time (May 2009).
The pdf scans I made there are what was used in the 3D Realms Anthology. None of the Anthology "manuals" were new materials - they were all re-uses of what I did in the past, either from a proper manual scan, or a scan of an old hint sheet.
So your use of "manual" was somewhat confusing to me - I'm guessing by "manual" you mean both of them.