Maybe you could move it somewhere else and see if any program gets grumpy. Try keeping it out of D for a day or two while you use ALL your programs and then if no problems crop up, you may go ahead and delete it.
tell me one thing Generic Superhero,what is the size of your hard disk? most probably atleast 40Gb?
so i think u should let this small 5 kb file remain there!!!
jokes apart,you can rename it or move it someplace else and check the stability..