CAN'T COPY+PASTE A PROJECT FOLER

So, I've hit that "dang, I should convert this from Rm2k to Rm2k3" point in game development, but there has been a few times where the conversion process will mess up the game, so I've gotten in the habit of making a copy of my project folder and converting that game to Rm2k3.

Normally, this works fine, but for some reason it just won't work on one of my games. It's been on different computers and external hard drives, since I've worked on it at different places, but for some reason when I copy and paste the folder of the most recent version, the new project folder opens up in the editor (Rm2k and Rm2k3) as a really old version. There are maps missing, maps with older names, older chipsets appear, I'm even thinking the database might be an older version. I don't get why this is happening, and I don't want to risk messing up my original game folder by converting it. I have copied and pasted it half a dozen times to different folders, places like My Documents, and it will still appear to have recent files inside, but will open in the editor at the development stage it was at months ago.

Any idea what the heck is going on?