When placing a yellow-background Activity card (which does not list a city), the rulebook states:

• "These are generic activities, and a player chooses separately for each of these cards whether to count it as Tokyo or Kyoto."
• There is no indication that this choice can be changed later; the context implies the choice is made at the time the card is placed for the purposes of scoring and Train token placement.

Additionally, the rules on page 6 specify:
"Once a card is placed, it may NOT be discarded, moved to a different day, or swapped with the position of another card in the same day."

Summary

The city designation for a yellow-background Activity card is chosen when the card is placed and is permanent for all future purposes, including scoring and Train token placement.

Source:
Page 13 (yellow-background Activity cards and city choice), Page 6 (card placement is final)

Source: Base Rules (pp. 13, 3, 4, 6, 7)