"Almost everything was missing," Vicarious [Visions] designer Dan Tanguay said to Ars in an interview. By "everything," he means all of the Crash games' source code and reference materials.
"The original engine was specifically built for PlayStation 1," Tanguay said. "Naughty Dog pushed [the PS1] to the limits. They made a fantastic engine for doing that. That engine didn't see the light of day beyond PlayStation 1, as far as I know, and it certainly wasn't usable by us. Any code, anything like that, we didn't have access to."
Thankfully for Vicarious, the team did uncover a crucial data set: all three games' 3D meshes, provided by both Sony and Naughty Dog as a series of hard drives. ("They were compressed in some wacky format that we had to decode," Tanguay pointed out.) Meshes don't make an entire game, of course—far from it. Data on the original games' animations, characters, artificial intelligence, control timing, textures, and even a lot of the music was gone (though Tanguay confirms some musical data was recovered to help the team lock into songs' timing and MIDI instrumentation layers).
The rest, Vicarious producer Kara Massie said, came down to eyeballing and video comparisons. Crash remaster prototypes would run alongside video footage of the original games to confirm timings.