If I disabled Indexing on both disk volumes, rebooted, then re-enabled Indexing, would that refresh the Indexes? It's not that index. The $Bitmap file is used by the NTFS file system to organize the raw data on the drive. If it's messed up, then Windows doesn't know where all the pieces of your files are.
Run the diskcheck without the sector-by-sector scan first, which is faster. That will repair the file system, if possible, but won't usually take hours to do so.
IMO. This is the best advice given, up to this point.
In addition, you should know that checkdisk is crap, and only writes over bad sectors, trashing the data contained within. Repairing the files system is the best option without using any other tools/utilities. But you may loose data.
If you want to save your disk and the data on it, then I suggest your purchase
Spinrite, and let it do it's magic. I've found NOTHING that will repair drives and recover formerly lost data better than Spinrite.
Good luck.