diff --git a/Source/cmQtAutoGeneratorInitializer.cxx b/Source/cmQtAutoGeneratorInitializer.cxx
index b02d872a42..89568c3879 100644
--- a/Source/cmQtAutoGeneratorInitializer.cxx
+++ b/Source/cmQtAutoGeneratorInitializer.cxx
@@ -361,11 +361,16 @@ static void SetupAcquireSkipFiles(cmQtAutoGenDigest const& digest,
 {
   // Read skip files from makefile sources
   {
-    const std::vector<cmSourceFile*>& allSources =
-      digest.Target->Makefile->GetSourceFiles();
-    for (cmSourceFile* sf : allSources) {
+    std::string pathError;
+    for (cmSourceFile* sf : digest.Target->Makefile->GetSourceFiles()) {
       // sf->GetExtension() is only valid after sf->GetFullPath() ...
-      std::string const& fPath = sf->GetFullPath();
+      // Since we're iterating over source files that might be not in the
+      // target we need to check for path errors (not existing files).
+      std::string const& fPath = sf->GetFullPath(&pathError);
+      if (!pathError.empty()) {
+        pathError.clear();
+        continue;
+      }
       cmSystemTools::FileFormat const fileType =
         cmSystemTools::GetFileFormat(sf->GetExtension().c_str());
       if (!(fileType == cmSystemTools::CXX_FILE_FORMAT) &&
@@ -540,9 +545,16 @@ static void SetupAutoTargetUic(cmQtAutoGenDigest const& digest,
     std::vector<std::vector<std::string>> uiFileOptions;
     {
       std::string const uiExt = "ui";
+      std::string pathError;
       for (cmSourceFile* sf : makefile->GetSourceFiles()) {
         // sf->GetExtension() is only valid after sf->GetFullPath() ...
-        std::string const& fPath = sf->GetFullPath();
+        // Since we're iterating over source files that might be not in the
+        // target we need to check for path errors (not existing files).
+        std::string const& fPath = sf->GetFullPath(&pathError);
+        if (!pathError.empty()) {
+          pathError.clear();
+          continue;
+        }
         if (sf->GetExtension() == uiExt) {
           std::string const absFile = cmSystemTools::GetRealPath(fPath);
           // Check if the file should be skipped