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After doing a complete scan disk, 49,000 bits were found to be in bad sectors.
Is there any way to get these bits back to their proper location? I clicked on the fix all errors button and did the long scan in safe mode, but this did not solve the problem.

Bad sectors = Dying Hard Drive
If scandisk found "Bad Sectors", not only are the sectors not recoverable, but it also means that your hard drive is starting to die.
I would immediatly contact your favorite computer company, tell them you need a new hard drive, and get them to transfer all the data from the dying drive to the new drive
Tim

if this drive is under warranty, get the
diagnostic program from the support download section of the manufacturers site, it will create a report, then call their customer service,for a free replacement.

Scandisk will try to recover the data in any bad areas it finds and move it else where, so unless you got error messages saying unrecoverable error, data was lost, don't worry. Windows is not trying to use those bad areas. Scandisk has now flagged them defective in the FAT32 tables so Windows does not use them. They still show up as bad in scandisk.
Do backup all your critical data if possible and backup the whole system. Go to the disk manufactures web site and down load their diagnostic tools and try running them. Some times they can correct these minor problems or tell you the real status of the drive.
Would also recommend booting from a Windows Startup diskette and running scandisk from there in DOS mode.

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