PrC IIRC updates your kernel once you save your scene.bin (a popup comes and asks you if you want to update the kernel, which happens when it notices the lookup table is out of date). I would suggest using Hojo to do it, unless you are specifically going to use PrC at some point, otherwise you would be downloading PrC for something that Hojo can already do (not to say you shouldn't use PrC, but Hojo is the only one of the two that allows you to simply change the enemy stats... someone needs to accidentally render Hojo obsolete since most of the other old mods/tools have had the same happen to them, and for good reasons
).
Hojo's way to fix the Kernel lookup data is done by going to File->Update Kernel File... and finding your kernel.bin in the FF7/Data/Kernel directory, and it should automatically update that file based on your current Scene.bin changes. You should probably update the kernel from now on, after every time you save your scene.bin in Hojo, just to be safe so that instances like that don't happen again
. If you need to use PrC for anything though, you will not need to remember to update the kernel, another reason Hojo should become fully outdated (or Hojo should get a way to automatically do this, but I still say an all-in-one program for the scene.bin would be full of win).