diff --git a/image_analysis/rotation_indexer/RotationIndexer.cpp b/image_analysis/rotation_indexer/RotationIndexer.cpp
index 6720f93d2..fa6c7e111 100644
--- a/image_analysis/rotation_indexer/RotationIndexer.cpp
+++ b/image_analysis/rotation_indexer/RotationIndexer.cpp
@@ -333,7 +333,14 @@ void RotationIndexer::RunIndexingLocked() {
             // promotion of the same kind, so it is not applied here.
             if (demote_class && ClassImposesLengthEquality(ls.system))
                 return LatticeSearch(cand, /*dist_tolerance=*/0.0);
-            if (!IsHexagonalSystem(ls.system) && IsMetricallyHexagonal(ls.primitive_reduced)) {
+            // A primitive hexagonal lattice is written in ONE setting, the one derived from its reduced
+            // cell, whichever route named the class. Its twelve equivalent settings are the same
+            // lattice, but the run is not indifferent to which it gets: the fractional-index gates of
+            // the refinement and the axial-row count of the two-pass quality guard are not invariant
+            // under them, so a setting chosen afresh from each pass's strained cell lets the two
+            // passes differ in setting and the guard compare rows that are not the same rows.
+            if ((ls.system == gemmi::CrystalSystem::Hexagonal && ls.centering == 'P')
+                || (!IsHexagonalSystem(ls.system) && IsMetricallyHexagonal(ls.primitive_reduced))) {
                 ls.conventional = HexagonalConventional(ls.primitive_reduced);
                 ls.system = gemmi::CrystalSystem::Hexagonal;
                 ls.centering = 'P';