The only thing that happens, if you leave the pacifier to cool down in the boiling water is that scale from your water will attach to the pacifier and making it look dull. It’s harmless  and it will disappear again, but it looks dull. Another thing; don’t boil the pacifier again after initial sterilising. It will age and become sticky too quickly if you do. In daily care just wash it under running water and use a mild liquid soap. If it needs an extra thorough rinse place it in a strainer and pour boiling water over it.