Alrite thanks. I plan to spend some time today trying to figure this out. As always I appreciate your assistance.
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Alrite so I had a successful test. I took a scene.bin and opened it in PrC. I deleted (FFed out) the first 7 scenes. I checked the number of enemies in the scenes (some contain 1 and some BLANKs, some contain 2 and a BLANK, some contain only 2, and some contain 3 enemies). I then unpacked the altered scene.bin with Scene Reader. I made sure that I swapped a scene containing 3 enemies (scene82 with Guard Scorp) with another scene that also contained 3 enemies (scene97 with Corneo's Lackeys) - Just renamed them. Packed them back up - 264kb good - and opened repacked scene.bin in Hojo, checked the kernel, and made a new Disc1.bin. When I made it to the Guard Scorp battle, voila, Corneo's Lackey's showed up. So it seems that this method works.
I don't think it works if you switch a scene with 2 enemies with one containing 3 enemies. I also don't think it will repack to the correct file size if those first 7 scenes were not deleted. This attempt has worked, and hopefully future attempts will work. Now I can make a PSX version with Marlboros and Dragon Zombies as bosses and Materia Keepers and Red Dragons running around on the world map or in dungeons!!!
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Sidenote: I have heard that by doing this the Battle Square will cease to be functional. I hope not, but it may be a price I'm willing to pay.