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diff --git a/jstests/replsets/initial_sync_update_missing_doc1.js b/jstests/replsets/initial_sync_update_missing_doc1.js
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+++ b/jstests/replsets/initial_sync_update_missing_doc1.js
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+/**
+ * Initial sync runs in several phases - the first 3 are as follows:
+ * 1) fetches the last oplog entry (op_start1) on the source;
+ * 2) copies all non-local databases from the source; and
+ * 3) fetches and applies operations from the source after op_start1.
+ *
+ * This test updates and deletes a document on the source between phases 1 and 2. The
+ * secondary will initially fail to apply the update operation in phase 3 and subsequently have
+ * to attempt to check the source for a new copy of the document. The absence of the document on
+ * the source indicates that the source is free to ignore the failed update operation.
+ */
+
+(function() {
+    var name = 'initial_sync_update_missing_doc1';
+    var replSet = new ReplSetTest({
+        name: name,
+        nodes: [{}, {rsConfig: {arbiterOnly: true}}],
+    });
+
+    replSet.startSet();
+    replSet.initiate();
+    var primary = replSet.getPrimary();
+
+    var coll = primary.getDB('test').getCollection(name);
+    assert.writeOK(coll.insert({_id: 0, x: 1}));
+
+    // Add a secondary node but make it hang after retrieving the last op on the source
+    // but before copying databases.
+    var secondary = replSet.add();
+    secondary.setSlaveOk();
+
+    assert.commandWorked(secondary.getDB('admin').runCommand(
+        {configureFailPoint: 'initialSyncHangBeforeCopyingDatabases', mode: 'alwaysOn'}));
+    replSet.reInitiate();
+
+    // Wait for fail point message to be logged.
+    var checkLog = function(node, msg) {
+        assert.soon(function() {
+            var logMessages = assert.commandWorked(node.adminCommand({getLog: 'global'})).log;
+            for (var i = 0; i < logMessages.length; i++) {
+                if (logMessages[i].indexOf(msg) != -1) {
+                    return true;
+                }
+            }
+            return false;
+        }, 'Did not see a log entry containing the following message: ' + msg, 10000, 1000);
+    };
+    checkLog(secondary, 'initial sync - initialSyncHangBeforeCopyingDatabases fail point enabled');
+
+    assert.writeOK(coll.update({_id: 0}, {x: 2}, {upsert: false, writeConcern: {w: 1}}));
+    assert.writeOK(coll.remove({_id: 0}, {justOne: true, writeConcern: {w: 1}}));
+
+    assert.commandWorked(secondary.getDB('admin').runCommand(
+        {configureFailPoint: 'initialSyncHangBeforeCopyingDatabases', mode: 'off'}));
+
+    checkLog(secondary, 'update of non-mod failed');
+    checkLog(secondary, 'adding missing object');
+    checkLog(secondary, 'missing object not found on source. presumably deleted later in oplog');
+    checkLog(secondary, 'initial sync done');
+
+    replSet.awaitReplication();
+    assert.eq(0,
+              secondary.getDB('test').getCollection(name).count(),
+              'collection successfully synced to secondary');
+
+    replSet.stopSet();
+})();