3rd Cafe (Twitter ARG)
(The OOC notes will likely contain spoilers for the 15th Sphere plot, as well as what fragments of it survive in the 16th. Please don't be surprised if you get spoiled for them.)
The Third, Fourth and Fifth Cafes, in the 15th Sphere, are slightly different than in the 16th Sphere. The 3rd Cafe, for example, condenses Unearthly Horrors and Twice Third Temple, while Dive Fall is shifted to the 5th Cafe. Cafe Crisis happens offscreen.
In the 3rd Cafe specifically, the main changes to the CaD are that Mr. Perez, who appears in Unearthly Horrors, leads directly into the Astoria raid and the Quartz Brain Cocktail, two of the earlier 'plot arcs' in Salvation of the Flies. Also, the 3rd Cafe apparently ends after the Halloween Gambit following an event called the 'Return of the Princes' (see 5th Cafe).
(This is actually mentioned by Jean in Otherworldy Adventure's DD-LUX01, in Bad Omens - tl;dr he mentions that while there are minor time issues, nothing major's changed from it.)
Other than that, some of the major differences in the 3rd Cafe would be that the 2nd 8 of the CaD, in the 15th Sphere known as 7, aka Jennifer Hepburn, seems to have a much worse reputation than in the 16th. Ex-44, or Nick Langley, also defected to Astoria for real instead of just being an undercover spy working for the Deep Corp, and ex-17, or Felix Blackwood, seems to have left the CaD to join a cult of Lucifer. There are other changes to the story, but they're going to go in the respective Cafes' OOC pages.