The short answer is "You can't".
As it was described to me by a CE, there is a log file or queue that these events are entered into that is a fixed length. When the event moves down the queue and reaches the end, it "falls on the floor" so to speak and goes away.
If this is truly the case, the red flags will go away as additional events enter the queue and push them out. The busier the event queue is, the sooner the events will fall out.
i believe it is possible. if you click on the flag next to Physical Display you get a windows where you can acknowledge specifc alert.
this of course only works when the actual events that cause them stop from happening. if you keep get them the flags come back.