The Iriver basically is acts as a external hard drive as it is, it is a drag and drop so I don't think removing it will matter in this case, and I have removed and replaced the HD's in these before so its not that I would 't open it.
In my experience you will get better results doing file recovery / formatting / etc. when you mount a drive directly to the motherboard of the PC you're using to run said utilities from. The iPod I mentioned was using Rockbox so it was also acting as a drag-and-drop device, but with the additional USB interface in between I was not able to successfully perform any of the above tasks until I removed the drive and mounted it directly.
That said, be very careful to read up on how your iRiver expects your HDD partition table to be written before you decide to delete and re-create new partitions and re-format. Hopefully it's not wacky like my old iPod was - this was the BS I had to deal with:
http://brianschrameck.com/how-to-align-partitions-on-an-upgraded-ipod-hard-drive-in-windowsBefore you do any of this though, try mounting the iRiver normally in Windows. Open an elevated command prompt (Start - type "cmd", right-click, Run As Administrator), then type
CHKDSK /R X: (Where "X" is the drive letter where your iRiver is mounted).
Run this overnight - it will take many hours. Adding the /R switch tells CHKSDK to recover and relocate information from any bad sectors it finds on the drive. As I said before though, this will work much more reliably if you pop the drive out and mount it to your PC directly. It's just a big pain in the ass...