You should be able to set displayed and non-displayed time limits for various things, e.g. the timed arrow switches in OoT, or maybe a dungeon that collapses/explodes if you don't beat it in the time limit.
Time Limits
I was thinking more like having two additional timers implemented: One that when it reaches zero, all secret flags onscreen are no longer triggerable, and another which would actually trigger them all.
If you just warped the player to another, identical screen in order to "remove" the secret flags, the blocks wouldn't be in the same positions as when you had warped. They'd be in their original places.
I like Shadow Tiger's flag idea. (Gets his own evil ideas) Any chance we can get this implemented?
before or after 2.5?
I would hope before, because this strikes me as simply adding an option on the Screen Data, and in the code just adding a "Timer" function somewhere. (Somthing like "After X ticks, activate all secrets", or "after X ticks, delete all flags" translated into code, which I don't think would be too hard)