I had this same problem when I cloned my site to set up a development server – for me, it working by setting permalinks to ugly, saving, then setting them to pretty again, which rebuilt whatever had gone wrong in htaccess.
I had this same problem when I cloned my site to set up a development server – for me, it working by setting permalinks to ugly, saving, then setting them to pretty again, which rebuilt whatever had gone wrong in htaccess.