Its not wise to use abbreviations in an international community, the dictionary lists several pages for "SOF" including "Sudent Orchestra Festival".
I saw one reset Pin in the top design Which project are you referring to?
What I an expecting is a signal kind of hardware connection to timer reset , that can be set from ISR easily You may use a control register to set a signal.
Easiest to help you would be when you post your complete project, so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.