I feel your pain. Same thing happened to me for our upcoming cruise. Only one of us is using the
DCL to the ship. Like you, there was no place to indicate that when I did online checkin for all of us. This had never been a problem for previous cruises so I think it is an oversight in the current update.
I called DCL to check. The agent could see the transfer including the WDW hotel and told me it was not a problem with the system.

When our cruise documents arrived and it was still not listed, I called again. Much better agent who could see her transfer but understood my concern. She emailed me a confirmation which showed the transfer, thank goodness. Good luck and happy sailing.