slknrm1

Quick update: changing the .gba and .fla file names to something else seems to work. But maybe there is an easier way than to keep changing the file names every time I edit something? Would also be nice to know the reason it didn't work with the same file name...

I have the same problem. Weird thing is, a few weeks ago I edited my Pokemon Ruby save and it worked just fine (back then I only edited EVs). I tried editing items and box pokemon today and had the same issue as you. I tried 1) saving over the old .fla file, 2) deleting the old .fla and pasting the new one, 3)same procedures but on Pokemon Gold (on my GBC Everdrive) and nothing worked. They all restore from where I had last saved in-game. In-game saving works fine. Have you figured it out?