The same thing happened to me the other day only in pokemon silver and pokemon gold on TGB dual (different emulators, same concept). When I finished with the trade from silver over to gold,
xender discord omegle I opened silver up on the gb1 slot on my tgb dual ( this is equvalent to window 1 in vba). When i tried opening my save file in gb1 slot on my emulator, I had all of the old pokemon that I supposedly traded over to gold still in my party. It's as if the trade never occurred. Also I noticed when I created a folder for vba ( I had played the files on vba before turning them into tgb files) every time I would open up a game, a new file would be created. You probably played the vba on window 1 instead of window 2 causing it to open up the file you had before the trade. try opening the game on window 2. I hope this helps and I don't sound like an idiot pretending to be smart.