It seems to work for me.
I took a PDF file I had added annotations to in Reader and changed its name.
In the Documents view, click the Edit button, then select the file (a red checkbox appears). Click the Rename icon (box with an I-bar icon, to the left of trash can). It will let you rename the file.
Perhaps the file was secured (locked)?
I've checked the file awhile ago, it isn't locked. I'm using adobe reader on ipad3, does it have the function of saving newly edited pdfs under a different file name? I just tried to draw something on the pdf and when i click save to finalise the drawing, it saved directly onto the file automatically without any options to save under a different name. Does it have a option to save it under a different file name? Or i have to duplicate the file everytime before i try to make any edits, just in case i want to revert to the original copy as there is no undo option as well?