Try using the USB loader itself to download your covers.
By default it will save the covers on SD:/config/images
Or you could either ask for your Backup Manager to download them for you, and move them to the SD card using this file structure, althought i would recommend using the loader on the WII since it will make all the structure for your and save each cover (HD, 3D, Full, Disc) to their respective folders.
To be honest i never heard of a case of a read-only HD due to hardware fault. But i think it might be possible.
Anyways I´d try other stuff though. Did you mess with the permisions while you were using the HDD on windows? Is it a NTFS or FAT32 partition?
Also, if you are gonna buy a new HDD, try getting a regular 2.5'' SATA HD and put it in an USB enclosure. Its cheaper this way, and easier to mantain in the future.
Hope this helps.