Hatch timers are of two varieties, first egg to hatch- how long it takes pet to hatch so you can train/equip; usually the longer the hatch time the higher pedigree or rarer the pet is inside of the egg. The other is timer to be able to hatch pets at the hatchery, either 12 or 24 hours for cool down unless you buy crown item that does immediate cool down. Neither of these affect your equipped pet or any other pet you have.