I would put caulk in the gap, because it won't crack.
A: Ah, but you have to use the right type of caulking and you have to fill the void properly. If you are going to do the job do it all around the pool at one time. You might find the right ingredients in a full service pool store or a rock & gravel supply yard. Ask for Deck-o-seal. The product is expensive but none other will do the job correctly. With that, there is a foam product which comes in various widths and depths. You may need a few different ones and enough to do the entire perimeter.
Once you have removed all the old caulking ( I mean ALL). Fill the void with maybe a # 20 sand up to within about 1" from the top of the deck. It may take a while to do this and in some cases you may never seem to fill the void. Use the foam that comes closest to filling the rest of the void BUT leaving, again, a depth equal to that of the width of the joint. Uniformity of depth and width are a key factor. Prep is the heart of your job - the better the prep the better the finished product will turn out. Pack the joint well - leaving no voids.
Have the supply place give you the instructions as how to use this product properly.
Once you have preped the deck joint and cleaned all the loose material including the sand away from the open joint, your next job is as important as the prep if not more so. Follow the manufacturer's instructions to the letter. DO NOT CUT CORNERS HERE OR YOU WILL REGRET EVEN STARTING THE JOB. THOROUGHLY mix part one as directed. Mix the can- part 2 - again as directed - the full ten minutes. Mix the 2 parts together and stir again as directed not a minute less than directed. If you can, squeeze the gallon container top - the one with the mix - until you have formed a small spout. You can pour from this spout or pour the compound into the plastic bottle provided for more control. You may want more than one bottle. It takes a steady hand to pour this thick product into that little joint but with practice you can do it. Just don't over pour or drop any onto the surrounding deck. And remember not to walk or step into the newly poured caulk. Keep kids, people, pets from this area until the mix has cured solidly. This is where you may have to include a cleaner at time of purchase of the sealant. Make sure that before you start mixing the product that you are in fact ready to begin the job for once you start you don't have time to dedo things. You have a set time to pour what you have mixed before it starts setting up.
Note: the longer you leave the open expansion joints undone the worse the deck will get. It will eventually start to heave because of the voids. Rain water gets into these open joints making the void larger. And oh yes - the deck and joint have to be absolutely dry. Read and re-read the entire label to get familiar with how to handle this product.
To make your job look a little more professional looking - sprinkle a fine clean sand over the finished joint compound after it has begun setting up but is still fairly sticky. If the sand is sprinkled too early it will sink into the compound. The caulking comes in 2 or 3 colors. Try to avoid the white - it will stand out like a sore thumb and not look natural but that depends upon what your surrounding deck looks like.
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