Here's the diagram of the AIS system:
The parts circled red have been removed from your bike. The parts marked yellow are still fitted to your bike.
The AIS valve (1) will be open to the atmosphere at A, which is where the removed parts were once attached. When the valve opens this will allow unfiltered air to be drawn in to the airbox from this opening.
You will need to block the hole at A, or block the airbox end at point B so the airbox has no unfiltered connection to the atmosphere. Alternatively you can refit the parts in the red circle but use the blanking plate under the flange when fitting to the cylinder head. The final option is to remove everything (as Matt suggested) and block the hole (B) left behind in the airbox.
Don't panic though! You won't have sucked in much unfiltered air in 100Km, as for a lot of the time the AIS valve would have been shut anyway. It would be more of a problem long term.
Hope this helps explain things a bit better?