You are right that there is no option for implicit themes in our Upgrade wizard. This is because the selected distribution itself defines whether implicit styles will be used.
For example let suppose that we have created a project which uses implicit styles. If RadControls for WPF, v.2013.1.403.40 distribution is selected in the upgrade wizard this means that the project will no longer use implicit styles after the upgrade. If RadControls for WPF (No XAML), v.2013.1.403.40 distribution is selected in the upgrade wizard this means that the project will still use implicit styles after the upgrade.
I know that this is not clear enough for our clients, so we will do our best to improve the upgrade process for some of the next releases.
As for the deleted changes in your resource library this is expected because while upgrade we update all Themes files included in the project when it was created. If you have modified this files (in the directory structure which was created during project creation), during upgrade they will be replaced with the new version and all changes will be lost.
In order not to loose your changes you could create a custom folder in your project and copy all your modified Themes there.
You are right that it is a good idea to ask whether the Themes should be updated or not, so I will log this in our product backlog for future consideration.
the Telerik team