There is no way to fix a problem like this because there is no way to know where it should point to. The affected area of the hard drive is simply considered to be lost and scandisk asks you whether you want to save that area in a file or put it back into the pool of available disk space. Go ahead and put it back in the pool of available space, you will find the saved file of little use. A few notes about using scandisk. This was a simplified explanation of scandisk.
Recent versions detect a wider variety of problems and recommend solutions.
You are best off accepting the action scandisk suggests, whatever the problem is. The bigger your hard drive, the longer scandisk to finish. The difference between running a standard or thorough scandisk is significant in the time it takes and what it does. Standard scandisk simply tests the directory structure and usually completes quickly. Thorough takes much longer.