As of Pro Tools 2024.6, Freezing and then unfreezing a track with Auto-Align 2 ARA will clear the track’s alignment data.
Possible workaround:
- From the Auto-Align 2 editor Settings menu at the bottom of the UI, click `Export…` and save the alignments.
- After unfreezing, restore the exported alignments by the `Import…` option under the Settings menu.
- Then click "Import" from the dialog on the bottom right.
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