Hate to say this:
big trees can have enormous root systems .... was a major area of concern when I fought forest fires in the SW....smoldering roots would sometimes create a blast furnace like conditions underground, and be several *feet in diameter* and hundreds of feet long..... one step on a weak spot, and its game over...
that said ...I would start over ....remove all the stonework and dig out any leftover roots ....
sand is a good filler for rotting roots ..will also help in leveling ..... but it may take years for the sand to fill in the voids
