Are you talking about the OS configuration wizard in the Kodi GUI (system name, wifi, services, etc.) or the installer wizard used for selecting a target disk to install the OS to?
If the former, this is good and the box is booting okay and you have a clean Kodi environment (as /storage/.kodi was renamed out of the way). This was intentional to ensure there is no conflicts with add-ons compiled for Xorg not GBM. You can restore the previous config by stopping Kodi and swapping the folders around again; or if there are any issues, by stopping Kodi and moving specific bits of config back again (add-on settings, sources, passwords, etc.). Binary add-ons like screensavers/visualisers compiled for the Generic Legacy (Xorg) image are not compatible with the Generic (GBM) image so I would normally suggest the partial restore option, or swap folders back but deliberately nuke /storage/.kodi/addons/* then reinstall add-ons.
If the latter, no idea what's going on..