Probably very late for this reply, but I'll provide it anyway since someone else could find it via a google search some day. Hopefully you already figured this out and never got a reply.
When you rebuilt your GDI, you forgot to select the CDDA which is track04.raw in your screenshot. Instead you generated a 3 track disc which puts all of the game data in track03.bin, but there was no game data in track03.bin previously.
In a GD-ROM all data is stored at the end of the disc because the outside is spinning faster than the middle so data reads back more quickly there. This was done on the original system to improve loading times. In the case of games with CDDA, track 3 only contains the file table that tells the system where files are stored, all of the actual files are stored in the final track after the CDDA. In your game, there was 1 CDDA Track (track 4) so all of the game data is in track 5. The original track03.bin was just a file table followed by empty padding to fill up the disc.
In other words, all of your changes were supposed to be in track05, but instead the entire disc was in track03. The patch you generated would contain all of the game data, because your patch would turn an empty track file into a file containing all data. In your screenshot, tracks 04 and 05 are completely useless because GDIbuilder did not know about the CDDA and built you a 3 track disc. (You built over an existing image so the files are still there) By re-building the disc image with the CDDA present you would have gotten three files updated (disc.gdi, track03.bin and track05.bin) and all files would then be used as they were before. This is also important to note, because your patch would need to account for all 3 of those files changing.
I hope this makes sense.