If you change it to Ellie, I guarantee that it will get shortened to El at school, or possibly Els or Ellie-bellie, or smelly-Ellie, or any number of other versions. If you call her Elle (El), it will also get lengthened to Ellie, or Ella, or Ellie-boo, etc. And you will have no control over it. Also, chances are she'll be a stubborn little madam, and will decide herself age 4 that she wants everyone to call her El/Ellie/Princess Consuela Banana Hammock and will no longer answer to whatever you chose for her originally.
I called my dd Lena, but put Helena on the bc. In between reception and year 1, she decided she wanted to be called Helena, and she has been ever since (except to her German relatives who never seem to remember).
Leave Elle on the bc, call her Ellie as a nickname. That's what everyone will assume you're doing anyway. Don't get offended when doctors call her Elle (El) or when she brings home party invitations addressed to Ellie. And let her choose for herself when she's old enough. Imo, ellie is a cute nickname for a 6 year old, Elle (El) is a lovely, grown up, classic name for a 20/30/40 year old woman.