don't worry, the links associated with the prefetch folder will be returned within a few shutdowns and powerups after using your most common applications. Do not worry, the same way the folder is originally populated, so it will be again.

Rebooting windows only updates ONE prefetch file during boot = NTOSBOOT-B00DFAAD.PF This file is created after the first boot but you must wait for over 1 minute after windows starts up so the file can be fully written. The file is further optimized after the second boot +1 minute. The rest of your application prefetch files are not created until you launch that application and again not finalized until after the second launch of the application. This is all automatic. To further optimize the files go to "Start", "Run", Type Rundll32.exe advapi32.dll,ProcessIdleTasks. This can take 10-15 minutes to run but no notification will be given when it is finished. You will notice increased Harddrive activity while it is running wait until this stops. When this is finished in the "Run" box Type defrag c: -b and a dos box will appear wait until it is gone. These last two steps also happen automatically but at system idle times and every three days but to get you system back to it's optimized self it is recommended to do them now.