startupFcn with a Timer

I am making a GUI in App Designer where the user is able to select the day and time the timer starts and how long they want the timer to run; however, I have all of the properties of the timer set up in the startupFcn, but the user selects how long they want it to run after the timer is already set up. The default for how long the timer runs is 1 hour, and so even if the user selects a different number (say 9 hours), it doesn't run for the amount of time the user selects it to be, only runs for an hour. Any other ways on how I should fix this? I tried putting the timer in other places besides the startupFcn, but errors keep popping up.

[Allen]

@Chloe Soriano please provide additional details regarding how your app is setup and possibly code from your startupFcn and callback functions for objects related to the user changing the timer duration value.