It sounds as though you're getting the initial indications of a failing drive. You could download a disk check program from the disk manufacturer, or run something like Spinright to give you more information. WHS itself can't diagnose any problems, you need a SMART program to check, WHS can only report when it gets problems writing.
As this is disk 2, that would indicate it's a data pool drive; therefore, if you have the available space, which it sounds as though you do, then just mark it for removal. It can take hours (and hours,) to complete, so be ready for a long wait. I've no idea why it should take so long, but it sometimes does.
I wouldn't remove the duplication, unless you think the drive might fail prior to getting a new one, as you could end up with the single copy of whatever on that failing disk.
Colin