If the job is done by a contractor - make a written contract.
First the odd stuff has to be removed with a router and (for the corners) a drill with a flexible axis and a router bit atached to it. You need goggles, mask and gloves as well as several bits/heads for the router, hidden nailing is the enemy.
When the grouts are clean-use a hoover- refill them with an apropiate filler, mind the shrinkage rate (label!). Take care that the boards are fixed well, if they move when walking on them the stuff might fall out again. The alternative would be rope (sisal, jute, hemp, coir) soaked in glue. Or lacquer to influence the final colour, black or green might give an interesting contrast. This rope would be forced into the groute similar to ship planks sealing with the aid of a chissel. When dry sand it over and fill the remaining gaps.
Calculate an hour for about 4-5 meters of groute for the entire job-removing, filling, sanding, finish.
Wear a good mask, one never knows with old timber how it was treated, DDT was a common timber treatment 30 years ago.