I have a similar issue. I have chiseled out the joints approx 1/2" (to 1" in places) to a firm base. The flagstones (sandstone in random pattern) were laid in mortar on a concrete slab about ten years ago and are firm. What should I use for mortar (this is only 8' x 6' area). My fear is the new mortar will not adhere to the old and come off during freeze/thaw cycles in this cold Toronto, Ontario, Canada area.