In the newest version of RRM3 (1fva81lji6dtr7-rrm3_installers_BETA_2023_06_29) animation on a rig controls that were in locked animation layers was not preserved after the rig has been rebuilt. On BaseAnimation layer it was ok (animation retained).
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In rrm3_installers_BETA_2023_07_07 I have added animLayers to be saved as part of the ATOM file that is generated which should preserve animLayer data. I tested it a bit and seemed to work properly. That being said, I strongly recommend only animating in the rig file for testing deformation. Any complex animation should be in a separate scene where the rig is referenced.