I don't know. Usually to overwrite files you need to format the Disc. If you didn't do that then the chances are the file shave been deleted "Windows Style" (ie not deleted, just forgotten about). In which case you can recover the files to the hard drive using IsoBuster and then re burn.
When you added the files did you "Import the Previous Session"? If not then you'll delete everything on the Disc when you burn. Next time "Import the previous session" and then you will ADD the new data to the Disc.