If you change the departure runway, the PERF page will prompt you to confirm the original speeds. As soon as you enter a new speed into any field the original data, including the FLEX temp is removed.
Often this occurs in a high workload situation and inserting the FLEX can be missed. Always check your FMA and if FLEX is not displayed simply go into TOGA.
A derated take off would be a different matter where the speeds assume the engines aren't giving full power and TOGA could give controllability issues with an engine failure.