So it’s perfectly plausible that she went and found him again off in the mountains, and played a deeper role in drawing Batman out.
Or maybe she died from the stab wound immediately after getting into the submarine. Who knows?
She was mostly there for Bruce, who skipped town soon after she did.
Nyssa’s exit probably would have felt more ominous and threatening had Gotham not been able to provide fans with that wonderful epilogue episode, but viewers can easily make assumptions about why she hadn’t returned to Gotham City in the ten-year interim.