diff --git a/mypy/build.py b/mypy/build.py
index 344221a3cfcc0..aad8b3a58e98a 100644
--- a/mypy/build.py
+++ b/mypy/build.py
@@ -1669,10 +1669,6 @@ def is_fresh(self) -> bool:
     def is_interface_fresh(self) -> bool:
         return self.externally_same
 
-    def has_new_submodules(self) -> bool:
-        """Return if this module has new submodules after being loaded from a warm cache."""
-        return self.meta is not None and self.child_modules != set(self.meta.child_modules)
-
     def mark_as_rechecked(self) -> None:
         """Marks this module as having been fully re-analyzed by the type-checker."""
         self.manager.rechecked_modules.add(self.id)
@@ -2405,11 +2401,6 @@ def load_graph(sources: List[BuildSource], manager: BuildManager,
                 if dep in st.suppressed:
                     st.suppressed.remove(dep)
                     st.dependencies.append(dep)
-    for id, g in graph.items():
-        if g.has_new_submodules():
-            g.parse_file()
-            g.fix_suppressed_dependencies(graph)
-            g.mark_interface_stale()
     return graph
 
 
diff --git a/mypy/server/update.py b/mypy/server/update.py
index e74e01738a221..6bdd9c3057fa5 100644
--- a/mypy/server/update.py
+++ b/mypy/server/update.py
@@ -399,8 +399,9 @@ def ensure_trees_loaded(manager: BuildManager, graph: Dict[str, State],
     """Ensure that the modules in initial and their deps have loaded trees."""
     to_process = find_unloaded_deps(manager, graph, initial)
     if to_process:
-        manager.log_fine_grained("Calling process_fresh_modules on set of size {} ({})".format(
-            len(to_process), to_process))
+        if is_verbose(manager):
+            manager.log_fine_grained("Calling process_fresh_modules on set of size {} ({})".format(
+                len(to_process), sorted(to_process)))
         process_fresh_modules(graph, to_process, manager)
 
 
diff --git a/test-data/unit/check-incremental.test b/test-data/unit/check-incremental.test
index 6856afc9400d0..acc0413c7f238 100644
--- a/test-data/unit/check-incremental.test
+++ b/test-data/unit/check-incremental.test
@@ -946,7 +946,8 @@ from parent import b
 
 [file parent/b.py.2]
 
-[stale parent, parent.a, parent.b]
+[stale parent.a, parent.b]
+[rechecked parent, parent.a, parent.b]
 
 [case testIncrementalReferenceExistingFileWithImportFrom]
 from parent import a, b
diff --git a/test-data/unit/fine-grained-modules.test b/test-data/unit/fine-grained-modules.test
index 21777daf656ee..c59e61fadf93e 100644
--- a/test-data/unit/fine-grained-modules.test
+++ b/test-data/unit/fine-grained-modules.test
@@ -436,6 +436,18 @@ main:1: error: Cannot find module named 'p.q'
 main:1: note: (Perhaps setting MYPYPATH or using the "--ignore-missing-imports" flag would help)
 ==
 
+[case testDeleteSubpackageWithNontrivialParent1]
+[file p/__init__.py]
+def g() -> None:
+    pass
+[file p/b.py.2]
+def foo() -> None: pass
+foo()
+[delete p/b.py.3]
+[out]
+==
+==
+
 [case testDeleteModuleWithError]
 import a
 [file a.py]