Manga Studio vs Comic Studio

One of the images I wrote out jpeg from manga-studio files yesterday. I overwrote the entire folder I put in jpeg images for this 4koma, I guess...but why?(I don't remember the name of the folder, so I'm not sure...) If you tried overwrote something, alert message should have been shown, shouldn't it?

At the moment, I'm working almost all the drawings with Manga Studio, against my principal (Scanning all the line works). It makes the assistant works via the web easier - a little bit. I don't know which is better/faster, though.