Thanks for the feedback!
I tried changing CD.DAT to "3" and launching the game, and I was able to confirm that the patch changes the CD to "1" if you start the game, or if you load a game immediately at the start and then go to Crius (the CD changes as you land, and the storyline video plays).
So the patch is working.. *but*, until you reach a scene that requires a different CD, you won't get the change CD prompt. This is the same behaviour you'd see if you had the actual CDs in the drive, but it means that until you reach an FMV sequence the game wouldn't check if you had the correct CD on the drive.
This got me thinking: besides the current no-cd logic (automatic CD change), we'd want the game to make a CD check, and prompt a CD change, right after a savegame is loaded. Maybe even update CD.DAT on your hard drive accordingly. I'll dig a bit more at the EXE and see what I can find, maybe I can tweak the CD-change logic a bit more.