hello folks, i'm very glad to see this thread still alive
@never: i use xvi32. the brunt of the work was done by a program i wrote which accepts 2 .eep files and spits out the differences.
@Mitsugari: the answer is to try it, i suppose. PJ64 does not use a proprietary saving technique for .eep files. it just writes the raw data. if whatever file you're using is 512 bytes, then it's probably the raw data just like a PJ64 .eep file.
anyway, the source code for the SM64 Editor has gone down a green pipe, forever lost
i've recently gotten the motivation to start eep editing again, albeit from scratch. maybe soon i'll once again have a skeleton eep editing program, which may lead to other things.