I presume that the pine floor is both the finish floor and the sub-floor so it is only supported every 16 inches by joists. This type of floor will deflect between the joists so filler can get stressed and crack and fall out when it's walked on. I have used epoxy mixed with wood floor, but this can not be used all over the floor, only in the bad spots, because the boards will be glued together and may cause cracking if the wood shrinks. General purpose epoxy in the recommended ratio with about twice the volume of fine edger dust all mixed together at once is what I use to make almost a putty that you knife into the gaps. It takes 4-7 hours to harden so I spread it at the end of the first day after the roughing off. I only use this in two or three rows at a time. What keeps regular wood patch in place is securing the boards so they don't move independently. If there is access from below, you can install blocking between the floor joists which will really make a difference for this type of floor. I charge extra and use strips of one half inch plywood glued and fastened in place with screws or staples so sub-floor adhesive from a caulking gun can hold everything together when it dries.This will prolong the life of the floor, also, because the floor will not crack when it gets sanded thin, at the top of the groove. With a solid floor, I have put wood patch into a caulking gun and filled major gaps between boards that are fastened down so they move in unison.
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