Not to sure exactly what you meant, but I re-installed Eclipse. It seemed, however, that the user preferences remained, so I assumed there was something in the forge stuff that saved Eclipse preferences. moved a folder called .metadata out of the folder in
C:\Users\MyUser\Desktop\MC Modding - 1.6.4\forge\mcp\eclipse
(the eclipse folder is where I'm running my workspace, btw) and ran it again. This time, the user preferences were gone, and a new .metadata folder was made in the right location, however, my source folder was not showing up.
I'm just going to back up all my mod stuff and re-download forge (using 1.6.4 version)
Edit: I went ahead and reinstalled forge and eclipse.. and it worked