If you did exactly that, there's no reason BI would stop working. It would only stop working if you deleted the bi/data folder or if you overwrote files *inside* bi/data with metw files, both of which are not parts of the correct procedure.
Does the installer work for you (as in, does it extract the files)? If so, the only thing you need to do is run it and direct it to your *main* RTW directory (not the BI subdirectory or any other). Creating the shortcut for the mod is simple, you just create a new BI shortcut and append its Target line with " -mod:bi/metw -show_err -nm", so that it looks like this:
obviously "D:\Games\Rome - Total War" may differ depending on where you have RTW installed.Code:"D:\Games\Rome - Total War\RomeTW-BI.exe" -show_err -nm -mod:bi/metw