If Singapore and Kuala Lumpur is connected by high speed rail within 90 mins, there will be no direct flight between both cities.
There are evidences that two big cities connected within 90 mins by ground transporations have no flight, much less between intermediate stations.
Here are some examples
・Taiwan(Taipei - Kaohsiung)
Train: By Taiwan HSR, 93 mins(fastest) between Taipei and Zuoying
Flight: Before inauguration of Taiwan HSR, there were 50 flights per day between Taipei(Taoyuan or Songshan) and Kaohsiung
→5 years after inauguration of Taiwan HSR, flight route itself disappeared(except for connection flight for international flights)
・Japan(Tokyo - Sendai)
Train: By Tohoku Shinkansen, 91 mins(fastest) between Tokyo and Sendai
Flight: Before inauguration of Tohoku Shinkansen, there were some flights per day between Tokyo Haneda and Sendai
→3 years after inauguration of Tohoku Shinkansen, flight route itself disappeared(except for extra flights after Tohoku Earthquake)
・South Korea(Seoul - Daegue)
Train: By KTX, 94 mins(fastest) between Seoul and Dong-Daegue
Flight: Before inauguration of KTX, there were one flight per hour between Seoul Gimpo and Busan
→3 years after inauguration of KTX, flight route itself disappeared
・Europe(Paris - Brussels)
Train: By Thalys, 80 mins(fastest) between Paris Nord and Brussels Central
Flight: Before inauguration of Thalys, there were one flight per hour between Paris CDG and Brussels
→7 years after full inauguration of High Speed Rail, flights decreased to only one per day
