I have just updated 2 ds twos and it worked fine for me.
Here is what i did:
1. Backed up the games and saves.
2. Formatted the SD Card.
3. Copied the files from DSTWO_v1.10_eng.zip on to the SD.
4. Copied the files from Firmware_v1.08_eng.zip on to the SD.
5. The SD card looks like this:
6...