If you keep it in your PC, it will stay forever but only as long as it is in the PC. Once you take it out, the countdown starts. You have either 24, 48, 72, or 96 hours before it disappears(chosen at random). This also counts time you are not playing. So if you leave Zekrom in your party, turn off the game for a week and turn it back on, it will be gone. And NO, putting Zekrom back in the PC and taking it out will not reset the counter. It will only pause and then continue from where it left off.
Note: When PokeRus disappears, only the ability to spread goes with it. You still get double Effort Values.