diff --git a/mercurial/commands.py b/mercurial/commands.py
--- a/mercurial/commands.py
+++ b/mercurial/commands.py
@@ -3076,7 +3076,7 @@ def debugobsolete(ui, repo, precursor=No
                                 'of transaction.'))
 
         with repo.lock():
-            n = repo.obsstore.delete(indices)
+            n = repair.deleteobsmarkers(repo.obsstore, indices)
             ui.write(_('deleted %i obsolescense markers\n') % n)
 
         return
diff --git a/mercurial/obsolete.py b/mercurial/obsolete.py
--- a/mercurial/obsolete.py
+++ b/mercurial/obsolete.py
@@ -628,30 +628,6 @@ class obsstore(object):
         transaction.hookargs['new_obsmarkers'] = str(previous + len(new))
         return len(new)
 
-    def delete(self, indices):
-        """Delete some obsmarkers from store and return how many were deleted
-
-        Indices is a list of ints which are the indices
-        of the markers to be deleted."""
-        if not indices:
-            # we don't want to rewrite the obsstore with the same content
-            return
-
-        left = []
-        current = self._all
-        n = 0
-        for i, m in enumerate(current):
-            if i in indices:
-                n += 1
-                continue
-            left.append(m)
-
-        newobsstore = self.svfs('obsstore', 'w', atomictemp=True)
-        for bytes in encodemarkers(left, True, self._version):
-            newobsstore.write(bytes)
-        newobsstore.close()
-        return n
-
     def mergemarkers(self, transaction, data):
         """merge a binary stream of markers inside the obsstore
 
diff --git a/mercurial/repair.py b/mercurial/repair.py
--- a/mercurial/repair.py
+++ b/mercurial/repair.py
@@ -17,6 +17,7 @@ from . import (
     changegroup,
     error,
     exchange,
+    obsolete,
     util,
 )
 
@@ -313,3 +314,32 @@ def stripbmrevset(repo, mark):
                      "ancestors(head() and not bookmark(%s)) - "
                      "ancestors(bookmark() and not bookmark(%s))",
                      mark, mark, mark)
+
+def deleteobsmarkers(obsstore, indices):
+    """Delete some obsmarkers from obsstore and return how many were deleted
+
+    'indices' is a list of ints which are the indices
+    of the markers to be deleted.
+
+    Every invocation of this function completely rewrites the obsstore file,
+    skipping the markers we want to be removed. The new temporary file is
+    created, remaining markers are written there and on .close() this file
+    gets atomically renamed to obsstore, thus guaranteeing consistency."""
+    if not indices:
+        # we don't want to rewrite the obsstore with the same content
+        return
+
+    left = []
+    current = obsstore._all
+    n = 0
+    for i, m in enumerate(current):
+        if i in indices:
+            n += 1
+            continue
+        left.append(m)
+
+    newobsstorefile = obsstore.svfs('obsstore', 'w', atomictemp=True)
+    for bytes in obsolete.encodemarkers(left, True, obsstore._version):
+        newobsstorefile.write(bytes)
+    newobsstorefile.close()
+    return n