The particle STAR files generated by the predict step should contain an additional column mbnMembraneId with the label of that membrane, which would be preserved by RELION upon importing. Something like:
data_particles
loop_
_rlnTomoName #1
_rlnTomoImportParticleFile #2
_mbnMembraneId #3 Optional membrane label
tomo_0001 membrain-pick/membrain_pick_output/Tomo0001_T1S1M12_clusters.star T1S1M12
tomo_0001 membrain-pick/membrain_pick_output/Tomo0001_T1S1M14_clusters.star T1S1M14
tomo_0001 membrain-pick/membrain_pick_output/Tomo0001_T1S1M16_clusters.star T1S1M16
tomo_0001 membrain-pick/membrain_pick_output/Tomo0001_T1S1M17_clusters.star T1S1M17