Fix unitary synthesis for 3+ q

crates/accelerate/src/unitary_synthesis.rs

@@ -372,7 +372,8 @@ fn py_run_main_loop(
                     None,
                     None,
                 )?;
-                out_dag = synth_dag;
+                let out_qargs = dag.get_qargs(packed_instr.qubits);
+                apply_synth_dag(py, &mut out_dag, out_qargs, &synth_dag)?;
             }
         }
     }

releasenotes/notes/fix-unitary-synthesis-3q-2b2de5305bfd11ff.yaml

@@ -0,0 +1,8 @@
+---
+fixes:
+  - |
+    Fixed a bug in the :class:`.UnitarySynthesis` transpiler pass, where blocks of
+    :class:`.UnitaryGate`\s of 3 qubits or more were not correctly synthesized.
+    This lead e.g. to the circuit being overwritten with the last processed block or
+    to internal panics when encountering measurements after a such a block.
+    Fixed `#13586 <https://github.com/Qiskit/qiskit/issues/13586>`__.

test/python/transpiler/test_unitary_synthesis.py

@@ -1050,6 +1050,18 @@ def test_qsd(self, opt):
         qc_transpiled = transpile(qc, target=target, optimization_level=opt)
         self.assertTrue(np.allclose(mat, Operator(qc_transpiled).data))
 
+    def test_3q_with_measure(self):
+        """Test 3-qubit synthesis with measurements."""
+        backend = FakeBackend5QV2()
+
+        qc = QuantumCircuit(3, 1)
+        qc.unitary(np.eye(2**3), range(3))
+        qc.measure(0, 0)
+
+        qc_transpiled = transpile(qc, backend)
+        self.assertTrue(qc_transpiled.size, 1)
+        self.assertTrue(qc_transpiled.count_ops().get("measure", 0), 1)
+
 
 if __name__ == "__main__":
     unittest.main()