Answer

A player can assign the city for each yellow-background (generic) card separately at each boundary; they do not need to be consistent with earlier choices for that card. The rulebook states:

• "Some cards have a yellow background and do not list a city. These are generic activities, and a player chooses separately for each of these cards whether to count it as Tokyo or Kyoto."
  (page 13)

This means:

• At each boundary between days (or between cards), when determining if a Train token is needed, the player can decide the city for the yellow card at that moment.
• There is no requirement to be consistent with previous or future choices for that card’s city assignment.

Therefore, if a player ends a day in Tokyo and begins the next day in Tokyo, and there is a yellow-background card at the boundary, the player can assign that card to Tokyo for both days to avoid placing a Train token.

Source: page 13.

Source: Base Rules (pp. 13, 16, 3, 7, 8)