In the disk version of DD there was a problem with the 1.33 patch that was quickly fixed in 1.34 which could reset the fog of war. Some people have had a problem with the fog of war being completely clear entering the Dark Forest for the first time.

If there was a problem with the actual file names or content in the BD saves, you'd think chkdsk would also have a problem with them on the hard drive, unless there is something weird going on with FAT32 vs NTFS.

Depending on the script, it shouldn't be terribly hard to modify it to use the command line version of 7-zip, or something.