How to avoid appending incremental number to filename
The Upload File Replace module should do the trick:


  Module Page Description
  
  This is a small utility module that automatically stops Drupal from
  renaming new files upload via filefield CCK. When 2 files with the
  same name exist, the older files will be renamed.


Edit: Sorry, I missed the part where you are expecting a prompt. According to the comment below, it is not possible.