diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index b292ff3965a..ac82fbba02c 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -879,6 +879,10 @@ namespace ts {
                         return oldProgram.structureIsReused = StructureIsReused.SafeModules;
                     }
                 }
+
+                for (const p of oldProgram.getMissingFilePaths()) {
+                    filesByName.set(p, undefined);
+                }
             }
 
             // update fileName -> file mapping
@@ -886,10 +890,6 @@ namespace ts {
                 filesByName.set(filePaths[i], newSourceFiles[i]);
             }
 
-            for (const p of oldProgram.getMissingFilePaths()) {
-                filesByName.set(p, undefined);
-            }
-
             files = newSourceFiles;
             fileProcessingDiagnostics = oldProgram.getFileProcessingDiagnostics();