diff --git a/mercurial/cext/parsers.c b/mercurial/cext/parsers.c
--- a/mercurial/cext/parsers.c
+++ b/mercurial/cext/parsers.c
@@ -319,7 +319,9 @@
 		return NULL;
 	}
 	if ((self->flags & dirstate_flag_has_file_mtime) &&
-	    self->mtime_s == other_s && self->mtime_ns == other_ns) {
+	    self->mtime_s == other_s &&
+	    (self->mtime_ns == other_ns || self->mtime_ns == 0 ||
+	     other_ns == 0)) {
 		Py_RETURN_TRUE;
 	} else {
 		Py_RETURN_FALSE;
diff --git a/mercurial/dirstateutils/timestamp.py b/mercurial/dirstateutils/timestamp.py
--- a/mercurial/dirstateutils/timestamp.py
+++ b/mercurial/dirstateutils/timestamp.py
@@ -5,15 +5,17 @@
 
 from __future__ import absolute_import
 
+import functools
 import stat
 
 
 rangemask = 0x7FFFFFFF
 
 
+@functools.total_ordering
 class timestamp(tuple):
     """
-    A Unix timestamp with nanoseconds precision,
+    A Unix timestamp with optional nanoseconds precision,
     modulo 2**31 seconds.
 
     A 2-tuple containing:
@@ -22,6 +24,7 @@
     truncated to its lower 31 bits
 
     `subsecond_nanoseconds`: number of nanoseconds since `truncated_seconds`.
+    When this is zero, the sub-second precision is considered unknown.
     """
 
     def __new__(cls, value):
@@ -29,6 +32,27 @@
         value = (truncated_seconds & rangemask, subsec_nanos)
         return super(timestamp, cls).__new__(cls, value)
 
+    def __eq__(self, other):
+        self_secs, self_subsec_nanos = self
+        other_secs, other_subsec_nanos = other
+        return self_secs == other_secs and (
+            self_subsec_nanos == other_subsec_nanos
+            or self_subsec_nanos == 0
+            or other_subsec_nanos == 0
+        )
+
+    def __gt__(self, other):
+        self_secs, self_subsec_nanos = self
+        other_secs, other_subsec_nanos = other
+        if self_secs > other_secs:
+            return True
+        if self_secs < other_secs:
+            return False
+        if self_subsec_nanos == 0 or other_subsec_nanos == 0:
+            # they are considered equal, so not "greater than"
+            return False
+        return self_subsec_nanos > other_subsec_nanos
+
 
 def zero():
     """
diff --git a/mercurial/pure/parsers.py b/mercurial/pure/parsers.py
--- a/mercurial/pure/parsers.py
+++ b/mercurial/pure/parsers.py
@@ -302,7 +302,9 @@
             return False
         self_ns = self._mtime_ns
         other_sec, other_ns = other_mtime
-        return self_sec == other_sec and self_ns == other_ns
+        return self_sec == other_sec and (
+            self_ns == other_ns or self_ns == 0 or other_ns == 0
+        )
 
     @property
     def state(self):
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
@@ -120,9 +120,17 @@
     /// If someone is manipulating the modification times of some files to
     /// intentionally make `hg status` return incorrect results, not truncating
     /// wouldn’t help much since they can set exactly the expected timestamp.
+    ///
+    /// Sub-second precision is ignored if it is zero in either value.
+    /// Some APIs simply return zero when more precision is not available.
+    /// When comparing values from different sources, if only one is truncated
+    /// in that way, doing a simple comparison would cause many false
+    /// negatives.
     pub fn likely_equal(self, other: Self) -> bool {
         self.truncated_seconds == other.truncated_seconds
-            && self.nanoseconds == other.nanoseconds
+            && (self.nanoseconds == other.nanoseconds
+                || self.nanoseconds == 0
+                || other.nanoseconds == 0)
     }
 
     pub fn likely_equal_to_mtime_of(