I would suggest trying to use the photorec[1] program on both the original SD card and the 2TB HDD to which you copied the files. It was specifically designed to recover from deleted files on removeable media. I'm not sure what happened with ext2fsd, but you might try seeing if ext2fsd can see the files if you reconnect the HDD back to the original computer. Note that very few people develop and use ext2fsd, so I can't really speak to how well it works.
[1] http://www.cgsecurity.org/wiki/PhotoRec
Most users will use Linux to read the FAT/VFAT formatted file system, and copy it to a ext2/3/4 file system, and not try to use Windows for that task. So unfortunately, use used the less travelled path, and ran into some kind of bug. :-(
Good luck!