Originally Posted by
Often1
... As to what did happen:
1. You are clearly entitled to a refund for the fare difference for the segment.
2. If the agent, in fact, refused to look for D1 availability you may have a claim under EC 261/2004 for downgrade reimbursement. That would amount to 75% of the base segment fare for JFK-SFO. That might be a nice chunk of change.
as I read OP's retelling of the events, the root cause of the misconnect was the delay passing through Customs & Immigration, which (I believe, having no experience in the matter) is in no way eligible for EC261 compensation from DL
any compensation for "If the agent ... refused to look for D1 availability" is entirely between OP and DL Customer Service