diff --git a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
--- a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
+++ b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
@@ -11,8 +11,8 @@
 
 #include "clang/Basic/LLVM.h"
 #include "clang/Lex/PreprocessorExcludedConditionalDirectiveSkipMapping.h"
+#include "llvm/ADT/DenseSet.h"
 #include "llvm/ADT/StringMap.h"
-#include "llvm/ADT/StringSet.h"
 #include "llvm/Support/Allocator.h"
 #include "llvm/Support/ErrorOr.h"
 #include "llvm/Support/VirtualFileSystem.h"
@@ -308,13 +308,15 @@
 
 private:
   /// Check whether the file should be minimized.
-  bool shouldMinimize(StringRef Filename);
+  bool shouldMinimize(StringRef Filename, llvm::sys::fs::UniqueID UID);
 
   /// Returns entry for the given filename.
   ///
   /// Attempts to use the local and shared caches first, then falls back to
   /// using the underlying filesystem.
-  llvm::ErrorOr<EntryRef> getOrCreateFileSystemEntry(StringRef Filename);
+  llvm::ErrorOr<EntryRef>
+  getOrCreateFileSystemEntry(StringRef Filename,
+                             bool DisableMinimization = false);
 
   /// For a filename that's not yet associated with any entry in the caches,
   /// uses the underlying filesystem to either look up the entry based in the
@@ -325,7 +327,7 @@
   /// Minimizes the given entry if necessary and returns a wrapper object with
   /// reference semantics.
   EntryRef minimizeIfNecessary(const CachedFileSystemEntry &Entry,
-                               StringRef Filename);
+                               StringRef Filename, bool Disable);
 
   /// Represents a filesystem entry that has been stat-ed (and potentially read)
   /// and that's about to be inserted into the cache as `CachedFileSystemEntry`.
@@ -401,7 +403,7 @@
   /// currently active preprocessor.
   ExcludedPreprocessorDirectiveSkipMapping *PPSkipMappings;
   /// The set of files that should not be minimized.
-  llvm::StringSet<> NotToBeMinimized;
+  llvm::DenseSet<llvm::sys::fs::UniqueID> NotToBeMinimized;
 };
 
 } // end namespace dependencies
diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
@@ -42,8 +42,9 @@
 }
 
 EntryRef DependencyScanningWorkerFilesystem::minimizeIfNecessary(
-    const CachedFileSystemEntry &Entry, StringRef Filename) {
-  if (Entry.isError() || Entry.isDirectory() || !shouldMinimize(Filename))
+    const CachedFileSystemEntry &Entry, StringRef Filename, bool Disable) {
+  if (Entry.isError() || Entry.isDirectory() || Disable ||
+      !shouldMinimize(Filename, Entry.getUniqueID()))
     return EntryRef(/*Minimized=*/false, Filename, Entry);
 
   CachedFileContents *Contents = Entry.getContents();
@@ -210,19 +211,18 @@
 }
 
 void DependencyScanningWorkerFilesystem::disableMinimization(
-    StringRef RawFilename) {
-  llvm::SmallString<256> Filename;
-  llvm::sys::path::native(RawFilename, Filename);
-  NotToBeMinimized.insert(Filename);
+    StringRef Filename) {
+  // Since we're not done setting up `NotToBeMinimized` yet, we need to disable
+  // minimization explicitly.
+  if (llvm::ErrorOr<EntryRef> Result =
+          getOrCreateFileSystemEntry(Filename, /*DisableMinimization=*/true))
+    NotToBeMinimized.insert(Result->getStatus().getUniqueID());
 }
 
-bool DependencyScanningWorkerFilesystem::shouldMinimize(StringRef RawFilename) {
-  if (!shouldMinimizeBasedOnExtension(RawFilename))
-    return false;
-
-  llvm::SmallString<256> Filename;
-  llvm::sys::path::native(RawFilename, Filename);
-  return !NotToBeMinimized.contains(Filename);
+bool DependencyScanningWorkerFilesystem::shouldMinimize(
+    StringRef Filename, llvm::sys::fs::UniqueID UID) {
+  return shouldMinimizeBasedOnExtension(Filename) &&
+         !NotToBeMinimized.contains(UID);
 }
 
 const CachedFileSystemEntry &
@@ -275,13 +275,15 @@
 
 llvm::ErrorOr<EntryRef>
 DependencyScanningWorkerFilesystem::getOrCreateFileSystemEntry(
-    StringRef Filename) {
+    StringRef Filename, bool DisableMinimization) {
   if (const auto *Entry = findEntryByFilenameWithWriteThrough(Filename))
-    return minimizeIfNecessary(*Entry, Filename).unwrapError();
+    return minimizeIfNecessary(*Entry, Filename, DisableMinimization)
+        .unwrapError();
   auto MaybeEntry = computeAndStoreResult(Filename);
   if (!MaybeEntry)
     return MaybeEntry.getError();
-  return minimizeIfNecessary(*MaybeEntry, Filename).unwrapError();
+  return minimizeIfNecessary(*MaybeEntry, Filename, DisableMinimization)
+      .unwrapError();
 }
 
 llvm::ErrorOr<llvm::vfs::Status>
diff --git a/clang/test/ClangScanDeps/modules-symlink.c b/clang/test/ClangScanDeps/modules-symlink.c
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/modules-symlink.c
@@ -0,0 +1,54 @@
+// RUN: rm -rf %t
+// RUN: split-file %s %t
+
+//--- cdb_pch.json
+[
+  {
+    "directory": "DIR",
+    "command": "clang -x c-header DIR/pch.h -fmodules -gmodules -fimplicit-module-maps -fmodules-cache-path=DIR/cache -o DIR/pch.h.gch",
+    "file": "DIR/pch.h"
+  }
+]
+
+//--- cdb_tu.json
+[
+  {
+    "directory": "DIR",
+    "command": "clang -c DIR/tu.c -fmodules -gmodules -fimplicit-module-maps -fmodules-cache-path=DIR/cache -include DIR/pch.h -o DIR/tu.o",
+    "file": "DIR/tu.c"
+  }
+]
+
+//--- module.modulemap
+module mod { header "symlink.h" }
+
+//--- pch.h
+#include "symlink.h"
+
+//--- original.h
+// Comment that will be stripped by the minimizer.
+#define MACRO 1
+
+//--- tu.c
+#include "original.h"
+static int foo = MACRO; // Macro usage that will trigger
+                        // input file consistency checks.
+
+// RUN: ln -s %t/original.h %t/symlink.h
+
+// RUN: sed -e "s|DIR|%/t|g" %t/cdb_pch.json > %t/cdb.json
+// RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
+// RUN:   -generate-modules-path-args -module-files-dir %t/build > %t/result_pch.json
+//
+// RUN: %python %S/../../utils/module-deps-to-rsp.py %t/result_pch.json \
+// RUN:   --module-name=mod > %t/mod.cc1.rsp
+// RUN: %python %S/../../utils/module-deps-to-rsp.py %t/result_pch.json \
+// RUN:   --tu-index=0 > %t/pch.rsp
+//
+// RUN: %clang @%t/mod.cc1.rsp
+// RUN: %clang -x c-header %t/pch.h -fmodules -gmodules -fimplicit-module-maps \
+// RUN:   -fmodules-cache-path=%t/cache -o %t/pch.h.gch -I %t @%t/pch.rsp
+
+// RUN: sed -e "s|DIR|%/t|g" %t/cdb_tu.json > %t/cdb.json
+// RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
+// RUN:   -generate-modules-path-args -module-files-dir %t/build > %t/result_tu.json