diff --git a/subcmds/sync.py b/subcmds/sync.py
index 57ee054..507d1c9 100644
--- a/subcmds/sync.py
+++ b/subcmds/sync.py
@@ -657,21 +657,27 @@
 
     tidy_dirs = {}
     for project in projects:
-      # Make sure pruning never kicks in with shared projects.
+      # Make sure pruning never kicks in with shared projects that do not use
+      # alternates to avoid corruption.
       if (not project.use_git_worktrees and
               len(project.manifest.GetProjectsWithName(project.name, all_manifests=True)) > 1):
-        if not opt.quiet:
-          print('\r%s: Shared project %s found, disabling pruning.' %
-                (project.relpath, project.name))
-        if git_require((2, 7, 0)):
-          project.EnableRepositoryExtension('preciousObjects')
+        if project.UseAlternates:
+          # Undo logic set by previous versions of repo.
+          project.config.SetString('extensions.preciousObjects', None)
+          project.config.SetString('gc.pruneExpire', None)
         else:
-          # This isn't perfect, but it's the best we can do with old git.
-          print('\r%s: WARNING: shared projects are unreliable when using old '
-                'versions of git; please upgrade to git-2.7.0+.'
-                % (project.relpath,),
-                file=sys.stderr)
-          project.config.SetString('gc.pruneExpire', 'never')
+          if not opt.quiet:
+            print('\r%s: Shared project %s found, disabling pruning.' %
+                  (project.relpath, project.name))
+          if git_require((2, 7, 0)):
+            project.EnableRepositoryExtension('preciousObjects')
+          else:
+            # This isn't perfect, but it's the best we can do with old git.
+            print('\r%s: WARNING: shared projects are unreliable when using old '
+                  'versions of git; please upgrade to git-2.7.0+.'
+                  % (project.relpath,),
+                  file=sys.stderr)
+            project.config.SetString('gc.pruneExpire', 'never')
       project.config.SetString('gc.autoDetach', 'false')
       # Only call git gc once per objdir, but call pack-refs for the remainder.
       if project.objdir not in tidy_dirs: