Alright, found an extension in the chrome web store.
https://chrome.google.com/webstore/detail/downloads-overwrite-exist/fkomnceojfhfkgjgcijfahmgeljomcfk

When download starts, it will overwrite the existing file without confirmation. Not perfect, but I think I can live with it.

Hi,
I'm currently using some poorly coded web system that only web-kit browsers can display properly. And when I try to download some click generated files from that system, the download filename is always the same.

What opera does is, if the file is already there in my "Downloads" folder, a numeric suffix is automatically appended to the file name ("(1)", "(2)", ...). This is rather annoying because I just hope to keep the latest copy of the file. Now I have to rename those files every time before I can use a local script to process the latest one.

Is there a way to change this behavior so I can get a prompt like "File already exists. Overwrite?"

Any advise is appreciated.