I think we solved an issue with service not starting here:
And now only cleanup. You can remove this %AppData%\Storj\Storagenode folder If you merged blobs folder to the blobs folder in the correct location, and the orders folder to the orders folder in your installation location (by default it’s "C:\Program Files\Storj\Storage Node\"), but you seems installed it to the "C:\Storj", so the orders folder should be there.
Just do not overwrite existing files during the merge, thus only new files will be added to the correct location.
This should prevent from disqualification for losing a new pieces while your node were running with a wrong config file.