I had this happen about two months ago and again last week. Both times, the GA in the first city was able to check me out, check me back in and get the second boarding pass to print. The first flight was ORF-ATL-CLT, which was all DL metal. The second was SCE-DTW-ATL, with the first flight being a Connection Carrier. I did not lose my seat assignments, nor my UG on the second flight either time.