normally you´ve got 2 options:
1. exporting with the same name as before (replace)
2. renamed it, so you´ve got a second version of the same clip.
If you named it exactly the same as the existing one, it should ask for replace. If this don´t work, the existing clip is opened in any other program or window.
Ahhh... thank you so much. I am new at using Media Encoder so I guess the file was still open within this program. Makes sense. Thanks so much!