You'd be better served leaving the decking beneath, placing cement tile backer board down on it, and using the thinnest flagstone you can find.
With a stone thickness of over an inch your weight will go up very quickly.
I'm curious, what are the dimensions of your beam-ledger board-joists, how far apart are the joists centered, did you use joist hangers on the ledger board or do they rest on top of it, and how did you fasten the ledger board to the existing structure?
These are very important answers that should be known prior to starting the work.

See ya,
Kelly