deepsouth said:
Hate to say this:
.I would start over ....remove all the stonework and dig out any leftover roots ....
That's super drastic Deepsouth. Yes, Deep is correct.. nothin you can do about the collapse of organic material, but you certainly can decide to pull pavers and top off where needed once a year, rather than digging up the whole yard and trying to remove half rotted roots Which is never gonna be successful.. you're never gonna get it all out anyway, which deep also said No pavement is ever guaranteed to stay level no matter how you prepare the top 2 ft of soil unless you're poring foundations.
Go to your local big box store and buy a 8ft long 2x, check it to make sure it's straight, and pick up$20 of sand. drag your beam around your patio and mark any drastically deep areas with chalk. Pry those areas up, sand them and Replace stone. It's a one day operation