Hi Nishit ,
Never tried increasing the timeout in run time and I think it will consider the change timeout from the next run. My suggestion for you is to follow the best practice of timer implementation rather increasing the timeout to meet the maximum execution time.
Here are few link that you can ..
https://success.outsystems.com/Documentation/10/Developing_an_Application/Use_Timers
There's also a Masterclass on Timers here: https://www.outsystems.com/learn/courses/43/master-class-on-best-practices-and-timers/?StartCourse=False
Regards,
-PJ-