diff --git a/mercurial/pure/parsers.py b/mercurial/pure/parsers.py
--- a/mercurial/pure/parsers.py
+++ b/mercurial/pure/parsers.py
@@ -483,6 +483,8 @@
                 flags |= DIRSTATE_V2_MODE_IS_SYMLINK
         if self._mtime_s is not None:
             flags |= DIRSTATE_V2_HAS_MTIME
+        if self._mtime_second_ambiguous:
+            flags |= DIRSTATE_V2_MTIME_SECOND_AMBIGUOUS
 
         if self._fallback_exec is not None:
             flags |= DIRSTATE_V2_HAS_FALLBACK_EXEC
diff --git a/rust/hg-core/src/dirstate/entry.rs b/rust/hg-core/src/dirstate/entry.rs
--- a/rust/hg-core/src/dirstate/entry.rs
+++ b/rust/hg-core/src/dirstate/entry.rs
@@ -43,7 +43,10 @@
     truncated_seconds: u32,
     /// Always in the `0 .. 1_000_000_000` range.
     nanoseconds: u32,
-    second_ambiguous: bool,
+    /// TODO this should be in DirstateEntry, but the current code needs
+    /// refactoring to use DirstateEntry instead of TruncatedTimestamp for
+    /// comparison.
+    pub second_ambiguous: bool,
 }
 
 impl TruncatedTimestamp {
diff --git a/rust/hg-core/src/dirstate_tree/on_disk.rs b/rust/hg-core/src/dirstate_tree/on_disk.rs
--- a/rust/hg-core/src/dirstate_tree/on_disk.rs
+++ b/rust/hg-core/src/dirstate_tree/on_disk.rs
@@ -465,6 +465,9 @@
         };
         let mtime = if let Some(m) = mtime_opt {
             flags.insert(Flags::HAS_MTIME);
+            if m.second_ambiguous {
+                flags.insert(Flags::MTIME_SECOND_AMBIGUOUS);
+            };
             m.into()
         } else {
             PackedTruncatedTimestamp::null()