diff --git a/src/neptune/new/cli/clear.py b/src/neptune/new/cli/clear.py
index 3a31a0963..419be8caf 100644
--- a/src/neptune/new/cli/clear.py
+++ b/src/neptune/new/cli/clear.py
@@ -32,7 +32,7 @@
 
 
 class ClearRunner(AbstractBackendRunner):
-    def clear(self, path: Path, force: bool = False):
+    def clear(self, path: Path, force: bool = False, clear_eventual: bool = True):
         container_manager = ContainersManager(self._backend, path)
         synced_containers, unsynced_containers, not_found = container_manager.partition_containers_and_clean_junk(path)
 
@@ -40,7 +40,7 @@ def clear(self, path: Path, force: bool = False):
 
         ClearRunner.remove_containers(not_found)
 
-        if offline_containers or unsynced_containers:
+        if clear_eventual and (offline_containers or unsynced_containers):
             self.log_junk_metadata(offline_containers, unsynced_containers)
 
             if force or click.confirm("\nDo you want to delete the listed metadata?"):
diff --git a/src/neptune/new/cli/commands.py b/src/neptune/new/cli/commands.py
index 92d26fc26..f7a4f51fb 100644
--- a/src/neptune/new/cli/commands.py
+++ b/src/neptune/new/cli/commands.py
@@ -150,7 +150,8 @@ def sync(
     neptune sync --project workspace/project --offline-only
     """
 
-    sync_runner = SyncRunner(backend=HostedNeptuneBackend(Credentials.from_token()))
+    backend = HostedNeptuneBackend(Credentials.from_token())
+    sync_runner = SyncRunner(backend=backend)
 
     if runs_names:
         logger.warning(
@@ -171,6 +172,10 @@ def sync(
     else:
         sync_runner.sync_all_containers(path, project_name)
 
+    clear_runner = ClearRunner(backend=backend)
+
+    clear_runner.clear(path, clear_eventual=False)
+
 
 @click.command()
 @path_option
diff --git a/src/neptune/new/cli/sync.py b/src/neptune/new/cli/sync.py
index 769516798..71bbde923 100644
--- a/src/neptune/new/cli/sync.py
+++ b/src/neptune/new/cli/sync.py
@@ -82,41 +82,41 @@ def sync_execution(
         container_id: UniqueId,
         container_type: ContainerType,
     ) -> None:
-        disk_queue = DiskQueue(
+        with DiskQueue(
             dir_path=execution_path,
             to_dict=lambda x: x.to_dict(),
             from_dict=Operation.from_dict,
             lock=threading.RLock(),
-        )
-        while True:
-            batch, version = disk_queue.get_batch(1000)
-            if not batch:
-                break
-
-            start_time = time.monotonic()
-            expected_count = len(batch)
-            version_to_ack = version - expected_count
+        ) as disk_queue:
             while True:
-                try:
-                    processed_count, _ = self._backend.execute_operations(
-                        container_id=container_id,
-                        container_type=container_type,
-                        operations=batch,
-                    )
-                    version_to_ack += processed_count
-                    batch = batch[processed_count:]
-                    disk_queue.ack(version)
-                    if version_to_ack == version:
-                        break
-                except NeptuneConnectionLostException as ex:
-                    if time.monotonic() - start_time > retries_timeout:
-                        raise ex
-                    logger.warning(
-                        "Experiencing connection interruptions."
-                        " Will try to reestablish communication with Neptune."
-                        " Internal exception was: %s",
-                        ex.cause.__class__.__name__,
-                    )
+                batch, version = disk_queue.get_batch(1000)
+                if not batch:
+                    break
+
+                start_time = time.monotonic()
+                expected_count = len(batch)
+                version_to_ack = version - expected_count
+                while True:
+                    try:
+                        processed_count, _ = self._backend.execute_operations(
+                            container_id=container_id,
+                            container_type=container_type,
+                            operations=batch,
+                        )
+                        version_to_ack += processed_count
+                        batch = batch[processed_count:]
+                        disk_queue.ack(version)
+                        if version_to_ack == version:
+                            break
+                    except NeptuneConnectionLostException as ex:
+                        if time.monotonic() - start_time > retries_timeout:
+                            raise ex
+                        logger.warning(
+                            "Experiencing connection interruptions."
+                            " Will try to reestablish communication with Neptune."
+                            " Internal exception was: %s",
+                            ex.cause.__class__.__name__,
+                        )
 
     def sync_all_registered_containers(self, base_path: Path) -> None:
         async_path = base_path / ASYNC_DIRECTORY
diff --git a/src/neptune/new/internal/disk_queue.py b/src/neptune/new/internal/disk_queue.py
index 6217c6047..69763d8f9 100644
--- a/src/neptune/new/internal/disk_queue.py
+++ b/src/neptune/new/internal/disk_queue.py
@@ -233,4 +233,5 @@ def __enter__(self):
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
+        self.flush()
         self.close()