One problem is that you cannot have two files with the same filename in any one directory. The burning software should catch this and either refuse to burn or prompt you to rename the files in question, but I have seen a few cases where a burning application attempted to overwrite the files by deleting the reference to them and then burning the new ones. It sounds like that's what may have happened here. My suggestion would be to give ISOBuster a shot at recovering the files. There are plenty of alternatives, but it should give you a good idea of what to expect.
Best of luck.
On a DVD-R I had about 100 pictures that I had burned from my digital camera. The other day I burned 17 more from my camera. This time they came up in the middle of some of the previous pictures I burned and those are gone. I thought maybe the space had run out on the DVD-R and this was what happened. But when I went to check the space left on the DVD-R there was plenty left. What could've happened to the deleted pictures?