Yes, Hyper Triggers affect ALL the triggers. The only thing Hyper Triggers change is how often the game checks to see if any conditions are met. Normally it checks all triggers every 1-2 seconds but now it checks them every 1/12 second.
By changing the Conditions (use a switch or bring, for example) of the Hyper Triggers and using less waits you can let the Hyper Trigger only affect all the triggers for a certain period. For example, you could change the Hyper Triggers to only affect the triggers for the first 8 seconds.
However you can't do this:
Condition:
- Time is At Least 10 Seconds
- Time is At Most 20 Seconds
Action:
Wait 0 Miliseconds (repeat 63 times)
Preserve Trigger
I'll explain why. Whenever the game is orderd to 'wait' X miliseconds it will start checking if any other trigger must be fired. So when you have 1 Hyper Trigger with 10 waits it will check 10 times which conditions for which triggers are met. When you use multiple Hyper Triggers with multiple waits they will constantly check each others conditions (which is always) so they will constantly fire each other.
However at a certain point all the waits have been 'used up'. The Hyper Triggers will not work anymore. With 3 Hyper Triggers this last incredible long, enough for a whole game. But with less waits that 'end time' will happen a lot sooner.
Now with the example Hyper Trigger I gave you the Hyper Trigger will start after 10 seconds. From that moment on it will keep checking and checking and checking conditions, even after 20 game seconds.
I hope this helped

. If not, well.. no problem just inplant the Hyper Triggers and you're ok.