diff --git a/check_api/src/main/java/com/google/errorprone/fixes/SuggestedFixes.java b/check_api/src/main/java/com/google/errorprone/fixes/SuggestedFixes.java
index 439b60676f6..5626d92f8f8 100644
--- a/check_api/src/main/java/com/google/errorprone/fixes/SuggestedFixes.java
+++ b/check_api/src/main/java/com/google/errorprone/fixes/SuggestedFixes.java
@@ -1309,8 +1309,10 @@ public CharSequence getCharContent(boolean ignoreEncodingErrors) throws IOExcept
     boolean warningInSameCompilationUnit = false;
     for (Diagnostic<? extends JavaFileObject> diagnostic : diagnosticListener.getDiagnostics()) {
       warningIsError |= diagnostic.getCode().equals("compiler.err.warnings.and.werror");
+      JavaFileObject diagnosticSource = diagnostic.getSource();
+      // If the source's origin is unknown, assume that new diagnostics are due to a modification.
       boolean diagnosticInSameCompilationUnit =
-          diagnostic.getSource().toUri().equals(modifiedFileUri);
+          diagnosticSource == null || diagnosticSource.toUri().equals(modifiedFileUri);
       switch (diagnostic.getKind()) {
         case ERROR:
           ++countErrors;