Currently this feature works only partly and looks more like a bug: installer will uninstall existing version of BornAgain only if the version of existing package and the package being installing are the same.
If versions are different, then new version of BornAgain will be installed on the system, but, due to wrong order in the PATH, old libraries will be used.
Solution might be:
1. either allow only one version of BornAgagin on the system (requires registry usage and some of struggling with NSIS installer)
2. play with order in the PATH to take latest version in a play
I think, option 1. is the best