Exporting to phy changes cluster channels

Start with the supplied script, especially read_phy, recording.set_probe, and export_to_phy, and inspect how channel_positions.npy is used before cluster_info.tsv is written. Reproduce the export with the shown analyzer and compare channel numbers before export with cluster_info.tsv afterward. Done means exported channel numbers match the analyzer and the resulting waveforms and quality metrics use the intended channels.

After manual curation, I'm recalculating cluster waveforms and some quality metrics using the script below. However, when I export to phy, the channel numbers are wrong. When I pause/debug the script before export_to_phy, channel numbers are correct, but inspecting cluster_info.tsv after exporting, they're different. I would fix this post-hoc, but because the channel numbers are wrong, the calculated waveforms and subsequent waveform based quality metrics are also incorrect. I'd very much appreciate any help!

                  rec_folder = Path(probe_folder, probe)
                        probe_number = find_numbers_in_string(probe)
                        phy_dir = rec_folder
                        ac_dir = Path(phy_dir, 'postprocessed')
                        ac_dir_wave = Path(ac_dir, 'waveforms')
                        ac_dir_phy = Path(ac_dir, 'phy')

                        if not os.path.isdir(ac_dir_phy):

                            waveform_folder = Path(phy_dir, "analyzer")
                            report_folder = Path(phy_dir, 'report')

                            # Load your sorted units from the Phy folder
                            sorting = read_phy(phy_dir)

                            # Get channel locations from .npy file
                            path_channel_location = Path(phy_dir, 'channel_positions.npy')
                            channel_locations = np.load(path_channel_location)
                            num_channels = channel_locations.shape[0]

                            # Load the original recording
                            recording = si.read_binary(Path(ses_folder, "ksData_probe" + str(probe_number[0]) + ".dat"),
                                                       sampling_frequency=fs,
                                                       num_channels=num_channels,
                                                       dtype="int16")

                            probe_64, locations = utils.gen_probe()
                            recording.set_probe(probe_64, in_place=True)

                            #recording.set_dummy_probe_from_locations(channel_locations)
                            recording.annotate(is_filtered=True)

                            sorting = remove_excess_spikes(sorting, recording)
                            sorting = remove_duplicated_spikes(sorting=sorting, censored_period_ms=0.5, method="keep_first")
                            #sorting = sorting.remove_empty_units()

                            print("building analyzer")
                            analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording, return_scaled=False)

                            analyzer.compute("random_spikes")
                            analyzer.compute("waveforms", save=True)
                            templates = analyzer.compute("templates", save=True)
                            analyzer.compute(
                                "spike_amplitudes",
                                peak_sign="pos"
                            )
                            analyzer.compute("noise_levels")

                            amp_cutoff = analyzer.compute(
                                "quality_metrics",
                                qm_params=dqm_params
                            )

                            print("Saving analyizer")
                            analyzer.save_as(format="binary_folder", folder=ac_dir_wave)
                            print("Exproting to phy")
                            export_to_phy(analyzer, output_folder=ac_dir_phy, copy_binary=False, additional_properties=['quality'], remove_if_exists=True)
                            print("Finished" + str(ac_dir_phy))