diff --git a/genkit-tools/telemetry-server/src/localFileTraceStore.ts b/genkit-tools/telemetry-server/src/localFileTraceStore.ts
index df51494e2f..ee08f0cbe8 100644
--- a/genkit-tools/telemetry-server/src/localFileTraceStore.ts
+++ b/genkit-tools/telemetry-server/src/localFileTraceStore.ts
@@ -115,18 +115,31 @@ export class LocalFileTraceStore implements TraceStore {
 
   async save(id: string, rawTrace: TraceData): Promise<void> {
     let trace = this.filter(rawTrace);
-    if (Object.keys(trace.spans).length === 0) {
-      return;
-    }
+    // if everything is filtered, it's probably the root.
+    const possibleRoot = Object.keys(trace.spans).length === 0;
     const mutex = this.getMutex(id);
     await mutex.waitForUnlock();
     const release = await mutex.acquire();
     try {
-      const existing = await this.load(id);
+      const existing = (await this.load(id)) || trace;
       if (existing) {
         Object.keys(trace.spans).forEach(
           (spanId) => (existing.spans[spanId] = trace.spans[spanId])
         );
+        // If it's one of those weird roots (internal span that we filter) we try to fix
+        // whoever was referencing it by making them root.
+        if (possibleRoot) {
+          Object.keys(existing.spans).forEach((spanId) => {
+            const span = existing.spans[spanId];
+            if (
+              possibleRoot &&
+              span.parentSpanId &&
+              !existing.spans[span.parentSpanId]
+            ) {
+              delete span.parentSpanId;
+            }
+          });
+        }
         existing.displayName = trace.displayName;
         existing.startTime = trace.startTime;
         existing.endTime = trace.endTime;
@@ -136,7 +149,7 @@ export class LocalFileTraceStore implements TraceStore {
         path.resolve(this.storeRoot, `${id}`),
         JSON.stringify(trace)
       );
-      const hasRootSpan = !!Object.values(rawTrace.spans).find(
+      const hasRootSpan = !!Object.values(trace.spans).find(
         (s) => !s.parentSpanId
       );
       if (this.index && hasRootSpan) {
diff --git a/genkit-tools/telemetry-server/tests/file_store_test.ts b/genkit-tools/telemetry-server/tests/file_store_test.ts
index 6d222b3690..9c05069d20 100644
--- a/genkit-tools/telemetry-server/tests/file_store_test.ts
+++ b/genkit-tools/telemetry-server/tests/file_store_test.ts
@@ -319,6 +319,7 @@ describe('index', () => {
         name: 'spanB',
         start: 2345,
         end: 3456,
+        status: 0,
       },
       {
         id: TRACE_ID_1,
@@ -326,6 +327,7 @@ describe('index', () => {
         name: 'spanA',
         start: 1234,
         end: 2345,
+        status: 0,
       },
     ]);
   });
@@ -374,6 +376,7 @@ describe('index', () => {
           name: 'flowA',
           start: 1,
           end: 2,
+          status: 0,
         },
         {
           id: TRACE_ID_1,
@@ -381,6 +384,7 @@ describe('index', () => {
           name: 'flowA',
           start: 1,
           end: 2,
+          status: 0,
         },
       ]
     );
@@ -399,6 +403,7 @@ describe('index', () => {
           name: 'flowA',
           start: 1,
           end: 2,
+          status: 0,
         },
       ]
     );
@@ -418,6 +423,7 @@ describe('index', () => {
           name: 'flowA',
           start: 1,
           end: 2,
+          status: 0,
         },
       ]
     );
@@ -469,6 +475,7 @@ describe('index', () => {
           name: 'flowA',
           start: 1,
           end: 2,
+          status: 0,
         },
       ]
     );
diff --git a/genkit-tools/telemetry-server/tests/utils.ts b/genkit-tools/telemetry-server/tests/utils.ts
index 69e2648fdb..607dede66c 100644
--- a/genkit-tools/telemetry-server/tests/utils.ts
+++ b/genkit-tools/telemetry-server/tests/utils.ts
@@ -40,6 +40,7 @@ export function span(
     instrumentationLibrary: { name: 'genkit' },
     spanKind: 'INTERNAL',
     attributes,
+    status: { code: 0 },
   } as SpanData;
 }