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:
  1. From the Auto-Align 2 editor Settings menu at the bottom of the UI, click `Export…` and save the alignments.

  2. After unfreezing, restore the exported alignments by the `Import…` option under the Settings menu.

  3. Then click "Import" from the dialog on the bottom right.