it totally depends why the E:\windows is there.
get a utility like diskmon or filemon, and monitor the machine for a while to see if anything is actually running from E before you play with it.
once you "think" it's ok to delete it, make a temp folder, and cut and paste it into the temp folder, if it hangs up you "might" be able to undo the paste, and put your files back.
most likely it's left over from a failed install. but be careful, I've gotten to systems that some random employee (probably the janitor) of a business installed, failed, and re-installed on a new disk without deleting the original bad copy.
