A quick p.s.
I just checked the Comboio Portugal website for train schedules for the Sud Expresso to Hendaye. It leaves Santa Apolonia at 21:18 and Oriente at 21:27.
If you are going to have a lot of time to kill between arrival into Lisbon and departure on the train, both train stations have luggage storage (what I don't know is whether they will be able to take something as big as a bike or a bike box). If you went straight to Oriente, you could spend the day along the river, going to the oceanarium, eating, sitting at a café, etc. (The Oriente train station is at the Parque das Nacoes, the site of the Lisbon Expo in the 90s, and it is now a huge riverfront park). If you decided you'd rather spend the day in the city, you'd be better advised to take the metro into Santa Apolonia, leave your bikes there, and then hop back on the metro and go two stops to Baixa-Chiado. From there you can visit a lot of Old Lisbon over the course of a few hour stroll, lots of ups and downs, beautiful views, old buildings, castles, etc.
Buen camino, Laurie