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Well, your were experienceing fragmentation. This is a phonomenon that causes sectors on the drive to be wasted to to everyday use (deleting and adding files and data). If your computer supports the 40GB hard drive, you shouldn't have to worry about any of those barriers. Older computers may experience problems if the BIOS is unable to address space on hard drived past a certain point, thus barriers. If Windows can see the entire 40GB, you are safe.
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Repair Windows XP Guide --- Resolutions
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