New Post: Undeploy application

Yes, it will be a problem to use the new build's output against the existing application. When there is already an application installed and deployed, you must always run the undeploy using the existing installed application's files, uninstall that existing MSI, then start the install and deploy process with the new build.

As I mentioned earlier, you can combine the old MSI uninstall and new MSI install into one upgrade step if you always update the MSI properties within the .btdfproj.

Thanks,
Tom