Which version of the editor were you using? The old one did things like that but I've never seen the new one act that way (Granted it doesn't save resistance changes, but that's a minor issue). You should always test and make backups frequently, even if you do trust the editor.

I do believe you owe Zyrthofar's editor an apology for slandering it, I just checked your first beta, you forgot to change the monsters used by the formations you fight on the airship. 
I've made plenty of backups plus using IPS files. I didn't slander his program, I just said it bugged my ROM, its a fact. Now, lets move on.
I used the version you sent me. It loads and displays all the data correcly, but I'm going to assume it doesn't put the data back in the ROM correctly. FF4/FF2us is VERY fickle with this type of data--no one believed me back in 2000 when I was deciphering it for my hack but maybe now they do. Anyway, this is a moot point since I'm not using the editor any longer. Back to doing things by hand.