I can think of three ways to do this.
1.) Have the passage refresh each time the boss attacks by adding a link command that loops back on itself. (this goes in the hook.) This should make the fight code reset (without resetting health)
2.) Have the timer reset. I personally don't know how to reset the timer, but I'm sure it is possible.
3.) Have more than one <<timer>> macro. This one is not recommended, as you will end up with a lot of code filling up your passage, making it very distracting while you edit it.
I'm sure someone else can give you a better answer, but I figure I might as well try to help.