diff --git a/packages/core/src/agent/runner.ts b/packages/core/src/agent/runner.ts
index 8738163b..ddfd3ac1 100644
--- a/packages/core/src/agent/runner.ts
+++ b/packages/core/src/agent/runner.ts
@@ -38,6 +38,10 @@ import {
   type SystemPromptMode,
 } from "./system-prompt/index.js";
 import type { AuthProfileFailureReason } from "./auth-profiles/index.js";
+import {
+  sanitizeToolCallInputs,
+  sanitizeToolUseResultPairing,
+} from "./session/session-transcript-repair.js";
 
 // ============================================================
 // Error classification for auth profile rotation
@@ -181,6 +185,10 @@ export class Agent {
         }
         return this.currentApiKey;
       },
+      transformContext: async (messages) => {
+        const sanitizedInputs = sanitizeToolCallInputs(messages);
+        return sanitizeToolUseResultPairing(sanitizedInputs);
+      },
     });
 
     // Load Agent Profile (if profileId is specified)
diff --git a/packages/core/src/agent/session/session-transcript-repair.test.ts b/packages/core/src/agent/session/session-transcript-repair.test.ts
index d162dbd4..39282e24 100644
--- a/packages/core/src/agent/session/session-transcript-repair.test.ts
+++ b/packages/core/src/agent/session/session-transcript-repair.test.ts
@@ -112,6 +112,28 @@ describe("sanitizeToolUseResultPairing", () => {
     expect(out.some((m) => m.role === "toolResult")).toBe(false);
     expect(out.map((m) => m.role)).toEqual(["user", "assistant"]);
   });
+
+  it("drops tool results with empty tool call id", () => {
+    const input = [
+      {
+        role: "assistant",
+        content: [{ type: "toolCall", id: "call_1", name: "read", arguments: {} }],
+      },
+      {
+        role: "toolResult",
+        toolCallId: "",
+        toolName: "read",
+        content: [{ type: "text", text: "invalid id" }],
+        isError: true,
+      },
+      { role: "user", content: "next" },
+    ] as AgentMessage[];
+
+    const out = sanitizeToolUseResultPairing(input);
+    const toolResults = out.filter((m) => m.role === "toolResult") as Array<{ toolCallId?: string }>;
+    expect(toolResults).toHaveLength(1);
+    expect(toolResults[0]?.toolCallId).toBe("call_1");
+  });
 });
 
 describe("sanitizeToolCallInputs", () => {
@@ -147,4 +169,20 @@ describe("sanitizeToolCallInputs", () => {
       : [];
     expect(types).toEqual(["text", "toolUse"]);
   });
+
+  it("drops tool calls with empty id even when input exists", () => {
+    const input = [
+      {
+        role: "assistant",
+        content: [
+          { type: "toolCall", id: "", name: "read", arguments: { path: "a" } },
+          { type: "toolUse", id: " ", name: "exec", input: { cmd: "pwd" } },
+        ],
+      },
+      { role: "user", content: "hello" },
+    ] as AgentMessage[];
+
+    const out = sanitizeToolCallInputs(input);
+    expect(out.map((m) => m.role)).toEqual(["user"]);
+  });
 });
diff --git a/packages/core/src/agent/session/session-transcript-repair.ts b/packages/core/src/agent/session/session-transcript-repair.ts
index 956653b2..d8417e60 100644
--- a/packages/core/src/agent/session/session-transcript-repair.ts
+++ b/packages/core/src/agent/session/session-transcript-repair.ts
@@ -58,6 +58,10 @@ function hasToolCallInput(block: ToolCallBlock): boolean {
   return hasInput || hasArguments;
 }
 
+function hasValidToolCallId(block: ToolCallBlock): boolean {
+  return typeof block.id === "string" && block.id.trim().length > 0;
+}
+
 function extractToolResultId(msg: Extract<AgentMessage, { role: "toolResult" }>): string | null {
   const toolCallId = (msg as { toolCallId?: unknown }).toolCallId;
   if (typeof toolCallId === "string" && toolCallId) {
@@ -118,7 +122,7 @@ export function repairToolCallInputs(messages: AgentMessage[]): ToolCallInputRep
     let droppedInMessage = 0;
 
     for (const block of msg.content) {
-      if (isToolCallBlock(block) && !hasToolCallInput(block)) {
+      if (isToolCallBlock(block) && (!hasToolCallInput(block) || !hasValidToolCallId(block))) {
         droppedToolCalls += 1;
         droppedInMessage += 1;
         changed = true;