The VN should look to use loose files instead as long as the characters are messed up in there. Copy-pasting a character in there should be able to do it.
Overwriting the data folder can be accomplished by drag and dropping the whole data folder on top of the existing data folder.
GARBro functions by pulling the VN assets right out of the executable. By extracting said assets next to the executable, and by making the assets stored inside the executable unreadable, the VN can be forced to read the extracted assets instead.
The Freem method is the preferred way to do it without hassle, since the assets are given as loose files.