Thanks for flagging it! Just to make sure I follow: there are two overwrite options - Overwrite File, and Overwrite BakeName. Overwrite BakeName will only replace objects in the target file that have the same BakeName as what you put into the component, but will leave everything else in the file untouched. In the example you’ve got there, there’s no BakeName provided, so it wouldn’t delete anything.
If you want to overwrite the file completely, does it work if you use this option?