Due to a bug, beginning a NewGame+ file will completely reset progress on that save file. We are working to fix this as soon as possible and will keep you all updated on the matter. Please avoid NewGame+ mode until this issue is resolved!
UPDATE DEC 21 2015 8:03PM PST: We've created a bundle of save files for each of the main NG+ tiers. You can download this bundle here: http://www.tastystewdios.com/download/saverestore.zip