Somewhere on this forum, there's a tool called ff7StoK (You'll have to look for it, as I don't have the link saved). It's purpose is to avoid this specific issue that you are running into after modifying the Scene.bin file.
You need to decompile the kernel.bin file to the same folder of the ff7StoK executable. When you run the tool, it will update the information on the kernel.bin2 file (One of the compiled files inside the kernel.bin).
After that, all you have to do is compile it again and replace your kernel.bin file with this new one. You have to do this every time you edit anything in the Scene.bin file. I can confirm that it works like a charm.
BTW, use ff7gzip to decompile/compile the bin files.