The special formula and procedure of making the Ink was a possession of the Guild of Ink Makers.
Obviously Gehn rediscovered the secret of making the Ink in the ruins of the D'ni City, in the process of reviving the Art and the D'ni civilization. While he was stranded on Riven, he attempted to formulate new Ink and paper, but had many failures. When he discovered the correct formula, he taught it to his Guilds (possibly the Guild of Bookmakers). In the Beetle Room there is a hymn to Gehn, thanking him for teaching the Rivenese the art of making the Ink.
Atrus had discovered that certain of the special properties of the Ink could be simulated with the right diffractive resonance of certain crystals. This could produce a visual link to an Age. Of course without the Ink, the link was only visual, as the crystals do not bind onto a particular Age.