The local train from San Sebastian to Hendaye is basically a local subway service. It runs frequently, it is cheap, and worrying about its schedule months from now is like worrying about the New York Subway's schedule months from now. So do not worry to much about it.
The same for the TER trains to Bordeaux. These are also just local mass transit services. This is a trip where I would just go to the station in San Sebastion, buy a ticket to Hendaye, and then in Hendaye cross the street to the SNCF station, buy a ticket to Bordeaux and get on the next train.