The reason I ask? 7 years ago, the newest version of SnagIt would be version 11. I fired up version 11.4.3 on my Windows 10 version 1809 machine. Enabled the timer, used it. Changed the duration of the setting, used it. Then disabled it without issue. It was an instantaneous settings change, no delays.
I did the same thing with SnagIt 2019. So I can't reproduce your problem.