I have my template files all copied to my theme for editing.
I just spent a a bit of time editing the file cart>empty.php for the last little while - wondering why the changes weren't taking hold. Finally looked and found that the file has been changed it's now called cart-empty.php
So I just checked through the templates folder there's at least a dozen file changes. Additions, deletions, etc., If you've edited a lot of template files you might want to check into all the changes.
I thought the whole idea of editing copies was so that updates didn't mess with your edits. Guess not always the case.