Force a file to overwrite instead of appending
The application is in complete control of how it saves files (overwrite v. append). The answer is to pre-clean your destination before you start whatever work flow you are doing in Capture One. There are any number of ways to accomplish that. 


use the rm command from the terminal
write a bash script that does something more complicated
write an applescript
create a new folder each time to point the application at
create a disk image via Disk Utility that you can clone and throw away when finished


These are just some of the ideas. I am sure there are other ways as well. Just need to find one that works for you.

A final thought, contact the makers of Capture One and make a case for why you would like them to change the software. Perhaps they will listen. :)

Good luck.