rsync does not replace symlink atomically, i.e, first it unlinks an old symlink and then creates a new symlink. There is short time when symlink does not exist at all. The attached patch against 3.0.4 fixes the issue. However, it has been tested on FreeBSD only. The patch is also available on
http://sysoev.ru/tmp/rsync.symlink.patch

--- generator.c 2008-08-31 20:51:29.000000000 +0400
+++ generator.c 2008-10-08 23:10:17.000000000 +0400
@@ -1556,9 +1556,40 @@
                                if (remove_source_files == 1)
                                        goto return_with_success;
                                goto cleanup;
+                       } else {
+                               char fnametmp[MAXPATHLEN];
+
+                               /* Replace the symlink atomically. */
+                               if (!get_tmpname(fnametmp, fname))
+                                       goto cleanup;
+                               if (!mktemp(fnametmp))
+                                       goto cleanup;
+                               if (do_symlink(sl, fnametmp) != 0) {
+                                       rsyserr(FERROR_XFER, errno, "symlink %s -> \"%s\" failed",
+                                               full_fname(fnametmp), sl);
+                                       goto cleanup;
+                               }
+                               set_file_attrs(fnametmp, file, NULL, NULL, 0);
+                               if (do_rename(fnametmp, fname) != 0) {
+                                       rsyserr(FERROR_XFER, errno, "rename %s -> %s failed",
+                                               full_fname(fnametmp), full_fname(fname));
+                                       goto cleanup;
+                               }
+                               if (itemizing) {
+                                       itemize(fname, file, ndx, statret, &sx,
+                                               ITEM_LOCAL_CHANGE|ITEM_REPORT_CHANGE, 0, NULL);
+                               }
+                               if (verbose)
+                                       rprintf(code, "%s -> %s\n", fname, sl);
+#ifdef SUPPORT_HARD_LINKS
+                               if (preserve_hard_links && F_IS_HLINKED(file))
+                                       finish_hard_link(file, fname, ndx, NULL, itemizing, code, -1);
+#endif
+                               if (remove_source_files)
+                                       goto return_with_success;
+                               goto cleanup;
                        }
-                       /* Not the right symlink (or not a symlink), so
-                        * delete it. */
+                       /* Not not a symlink, so delete it. */
                        if (delete_item(fname, sx.st.st_mode, del_opts | DEL_FOR_SYMLINK) != 0)
                                goto cleanup;
                } else if (basis_dir[0] != NULL) {