Missing config after update via VS Marketplace

After Visual Studio auto-updated the extension from 3.0.2 to the latest 3.2.0, the configured versions and options were missing (respectively not migrated).

On one of my systems I used the pre-release versions 3.1.0 and 3.2.0 and the migration worked without any issue. However, version 3.1.0, which contained the change of the Registry location, was never officially released. So the migration may have broken in between.