Index: clang-tools-extra/clangd/Compiler.cpp
===================================================================
--- clang-tools-extra/clangd/Compiler.cpp
+++ clang-tools-extra/clangd/Compiler.cpp
@@ -95,7 +95,7 @@
   if (auto VFSWithRemapping = createVFSFromCompilerInvocation(
           Clang->getInvocation(), Clang->getDiagnostics(), VFS))
     VFS = VFSWithRemapping;
-  Clang->setVirtualFileSystem(VFS);
+  Clang->createFileManager(VFS);
 
   Clang->setTarget(TargetInfo::CreateTargetInfo(
       Clang->getDiagnostics(), Clang->getInvocation().TargetOpts));
Index: clang/include/clang/Basic/FileManager.h
===================================================================
--- clang/include/clang/Basic/FileManager.h
+++ clang/include/clang/Basic/FileManager.h
@@ -175,6 +175,10 @@
   void fillRealPathName(FileEntry *UFE, llvm::StringRef FileName);
 
 public:
+  /// Construct a file manager, optionally with a custom VFS.
+  ///
+  /// \param FS if non-null, the VFS to use.  Otherwise uses
+  /// llvm::vfs::getRealFileSystem().
   FileManager(const FileSystemOptions &FileSystemOpts,
               IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS = nullptr);
   ~FileManager();
Index: clang/include/clang/Frontend/CompilerInstance.h
===================================================================
--- clang/include/clang/Frontend/CompilerInstance.h
+++ clang/include/clang/Frontend/CompilerInstance.h
@@ -82,9 +82,6 @@
   /// Auxiliary Target info.
   IntrusiveRefCntPtr<TargetInfo> AuxTarget;
 
-  /// The virtual file system.
-  IntrusiveRefCntPtr<llvm::vfs::FileSystem> VirtualFileSystem;
-
   /// The file manager.
   IntrusiveRefCntPtr<FileManager> FileMgr;
 
@@ -382,20 +379,8 @@
   /// @name Virtual File System
   /// {
 
-  bool hasVirtualFileSystem() const { return VirtualFileSystem != nullptr; }
-
   llvm::vfs::FileSystem &getVirtualFileSystem() const {
-    assert(hasVirtualFileSystem() &&
-           "Compiler instance has no virtual file system");
-    return *VirtualFileSystem;
-  }
-
-  /// Replace the current virtual file system.
-  ///
-  /// \note Most clients should use setFileManager, which will implicitly reset
-  /// the virtual file system to the one contained in the file manager.
-  void setVirtualFileSystem(IntrusiveRefCntPtr<llvm::vfs::FileSystem> FS) {
-    VirtualFileSystem = std::move(FS);
+    return *getFileManager().getVirtualFileSystem();
   }
 
   /// }
@@ -645,7 +630,8 @@
   /// Create the file manager and replace any existing one with it.
   ///
   /// \return The new file manager on success, or null on failure.
-  FileManager *createFileManager();
+  FileManager *
+  createFileManager(IntrusiveRefCntPtr<llvm::vfs::FileSystem> VFS = nullptr);
 
   /// Create the source manager and replace any existing one with it.
   void createSourceManager(FileManager &FileMgr);
Index: clang/lib/Frontend/ASTUnit.cpp
===================================================================
--- clang/lib/Frontend/ASTUnit.cpp
+++ clang/lib/Frontend/ASTUnit.cpp
@@ -1078,28 +1078,29 @@
   if (!Invocation)
     return true;
 
+  if (VFS && FileMgr)
+    assert(VFS == FileMgr->getVirtualFileSystem() &&
+           "VFS passed to Parse and VFS in FileMgr are different");
+
   auto CCInvocation = std::make_shared<CompilerInvocation>(*Invocation);
   if (OverrideMainBuffer) {
     assert(Preamble &&
            "No preamble was built, but OverrideMainBuffer is not null");
-    IntrusiveRefCntPtr<llvm::vfs::FileSystem> OldVFS = VFS;
     Preamble->AddImplicitPreamble(*CCInvocation, VFS, OverrideMainBuffer.get());
-    if (OldVFS != VFS && FileMgr) {
-      assert(OldVFS == FileMgr->getVirtualFileSystem() &&
-             "VFS passed to Parse and VFS in FileMgr are different");
-      FileMgr = new FileManager(FileMgr->getFileSystemOpts(), VFS);
-    }
+    // VFS may have changed...
   }
 
   // Create the compiler instance to use for building the AST.
   std::unique_ptr<CompilerInstance> Clang(
       new CompilerInstance(std::move(PCHContainerOps)));
-  if (FileMgr && VFS) {
-    assert(VFS == FileMgr->getVirtualFileSystem() &&
-           "VFS passed to Parse and VFS in FileMgr are different");
-  } else if (VFS) {
-    Clang->setVirtualFileSystem(VFS);
-  }
+
+  // Ensure that Clang has a FileManager with the right VFS, which may have
+  // changed above in AddImplicitPreamble.  If VFS is nullptr, rely on
+  // createFileManager to create one.
+  if (VFS && FileMgr && FileMgr->getVirtualFileSystem() == VFS)
+    Clang->setFileManager(&*FileMgr);
+  else
+    FileMgr = Clang->createFileManager(std::move(VFS));
 
   // Recover resources if we crash before exiting this method.
   llvm::CrashRecoveryContextCleanupRegistrar<CompilerInstance>
@@ -1136,10 +1137,6 @@
   // Configure the various subsystems.
   LangOpts = Clang->getInvocation().LangOpts;
   FileSystemOpts = Clang->getFileSystemOpts();
-  if (!FileMgr) {
-    Clang->createFileManager();
-    FileMgr = &Clang->getFileManager();
-  }
 
   ResetForParse();
 
Index: clang/lib/Frontend/CompilerInstance.cpp
===================================================================
--- clang/lib/Frontend/CompilerInstance.cpp
+++ clang/lib/Frontend/CompilerInstance.cpp
@@ -89,10 +89,6 @@
 
 void CompilerInstance::setFileManager(FileManager *Value) {
   FileMgr = Value;
-  if (Value)
-    VirtualFileSystem = Value->getVirtualFileSystem();
-  else
-    VirtualFileSystem.reset();
 }
 
 void CompilerInstance::setSourceManager(SourceManager *Value) {
@@ -297,13 +293,14 @@
 
 // File Manager
 
-FileManager *CompilerInstance::createFileManager() {
-  if (!hasVirtualFileSystem()) {
-    IntrusiveRefCntPtr<llvm::vfs::FileSystem> VFS =
-        createVFSFromCompilerInvocation(getInvocation(), getDiagnostics());
-    setVirtualFileSystem(VFS);
-  }
-  FileMgr = new FileManager(getFileSystemOpts(), VirtualFileSystem);
+FileManager *CompilerInstance::createFileManager(
+    IntrusiveRefCntPtr<llvm::vfs::FileSystem> VFS) {
+  if (!VFS)
+    VFS = FileMgr ? FileMgr->getVirtualFileSystem()
+                  : createVFSFromCompilerInvocation(getInvocation(),
+                                                    getDiagnostics());
+  assert(VFS && "FileManager has no VFS?");
+  FileMgr = new FileManager(getFileSystemOpts(), std::move(VFS));
   return FileMgr.get();
 }
 
@@ -1101,8 +1098,6 @@
                                    ImportingInstance.getDiagnosticClient()),
                              /*ShouldOwnClient=*/true);
 
-  Instance.setVirtualFileSystem(&ImportingInstance.getVirtualFileSystem());
-
   // Note that this module is part of the module build stack, so that we
   // can detect cycles in the module graph.
   Instance.setFileManager(&ImportingInstance.getFileManager());
Index: clang/lib/StaticAnalyzer/Frontend/ModelInjector.cpp
===================================================================
--- clang/lib/StaticAnalyzer/Frontend/ModelInjector.cpp
+++ clang/lib/StaticAnalyzer/Frontend/ModelInjector.cpp
@@ -82,8 +82,6 @@
 
   Instance.getDiagnostics().setSourceManager(&SM);
 
-  Instance.setVirtualFileSystem(&CI.getVirtualFileSystem());
-
   // The instance wants to take ownership, however DisableFree frontend option
   // is set to true to avoid double free issues
   Instance.setFileManager(&CI.getFileManager());
Index: lldb/source/Plugins/ExpressionParser/Clang/ClangExpressionParser.cpp
===================================================================
--- lldb/source/Plugins/ExpressionParser/Clang/ClangExpressionParser.cpp
+++ lldb/source/Plugins/ExpressionParser/Clang/ClangExpressionParser.cpp
@@ -309,8 +309,7 @@
   }
 
   // Make sure clang uses the same VFS as LLDB.
-  m_compiler->setVirtualFileSystem(
-      FileSystem::Instance().GetVirtualFileSystem());
+  m_compiler->createFileManager(FileSystem::Instance().GetVirtualFileSystem());
 
   lldb::LanguageType frame_lang =
       expr.Language(); // defaults to lldb::eLanguageTypeUnknown
Index: lldb/source/Plugins/ExpressionParser/Clang/ClangModulesDeclVendor.cpp
===================================================================
--- lldb/source/Plugins/ExpressionParser/Clang/ClangModulesDeclVendor.cpp
+++ lldb/source/Plugins/ExpressionParser/Clang/ClangModulesDeclVendor.cpp
@@ -671,7 +671,7 @@
   }
 
   // Make sure clang uses the same VFS as LLDB.
-  instance->setVirtualFileSystem(FileSystem::Instance().GetVirtualFileSystem());
+  instance->createFileManager(FileSystem::Instance().GetVirtualFileSystem());
   instance->setDiagnostics(diagnostics_engine.get());
   instance->setInvocation(invocation);