Summary

When encountering a 3+ qubit UnitaryGate, UnitarySynthesis currently replaces the whole dag with the definition of the block instead of appending it, see

Details and comments

This also leads to #13586 because the qubit/clbit interners are overwritten, but maybe more importantly this can lead to issues when multiple 3-qubit blocks are present in the circuit. E.g. running

import numpy as np
from qiskit.quantum_info import Operator
from qiskit.circuit.library import UnitaryGate
from qiskit import QuantumCircuit, transpile
from qiskit_ibm_runtime.fake_provider import FakeSherbrooke

backend = FakeSherbrooke()

x = QuantumCircuit(3)
x.x(2)
x_mat = Operator(x)

qc = QuantumCircuit(3, 1)
qc.unitary(x_mat, range(3))
qc.unitary(np.eye(2 ** 3), range(3))

tqc = transpile(qc, backend, optimization_level=0)
print(tqc.count_ops())

produces an empty circuit, since the last block implements the identity.

Some additional tests, such as the precise case of #13586 and a series of 3q UnitaryGates, should be added.