You could just use chkdsk on a Windows PC connected via usb. I have used chkdsk successfully in this way, I have also used a defrag program on both the internal storage and the SD card.

Connect via mass storage mode.

I would have thought it a good idea to connect with the N900 switched off to prevent it accessing either disk at the same time as Windows (not sure whether that matters), but I have found that I can no longer access either drive when the device is off (possibly since reflashing to PR1.2).