The bacteria population which is usually referred to as "being cycled" lives all over all surfaces which are in contact with your saltwater. So yes, when you change the filter, that new surface will be clear of bacteria and will need time for them to grow on it. But how much surface is on that filter pad vs. the rest of your system? I'm guessing its a fairly small proportion. Not enough to get worried about.
In fact a bigger issue is just having the tank there with no livestock in it. Remember that being "cycled" means your bacteria population is in equalibrium with the waste production of the other living things in the tank. During times when there are no fish in the tank, that waste production will be very low to non-existent. This effectively removes the food supply of the bacteria, so their population will decrease. So when you innitially add new fish, the population of bacteria will be too small to keep up. But again probably not a huge problem unless you added a bunch of fish at once.
In all cases though, just test your water when you make changes and you will be fine.