diff --git a/CHANGELOG.md b/CHANGELOG.md
index a01d2e0..484d0be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 
+### Fixed
+- **checkPaths false positives** — `checkPaths` now only validates inline code paths from `ROUTER.md`, not all scaffold files. Eliminates false `MISSING_PATH` errors from context docs, pattern files, and tool config files where backtick-wrapped strings are config values, IPs, annotation keys, or other non-path content. [#79](https://github.com/theDakshJaitly/mex/issues/79)
+
 ## [0.6.1] - 2026-06-14
 
 ### Added
diff --git a/src/drift/index.ts b/src/drift/index.ts
index e47bf4e..6017b2d 100644
--- a/src/drift/index.ts
+++ b/src/drift/index.ts
@@ -1,5 +1,5 @@
 import { readFileSync } from "node:fs";
-import { resolve, relative } from "node:path";
+import { resolve, relative, basename } from "node:path";
 import { globSync } from "glob";
 import type { MexConfig, DriftReport, DriftIssue, Claim } from "../types.js";
 import { extractClaims } from "./claims.js";
@@ -91,7 +91,11 @@ export async function runDriftCheck(
   }
 
   // Run checkers that work on claims
-  const pathIssues = checkPaths(allClaims, projectRoot, scaffoldRoot);
+  // Only check paths in ROUTER.md — other scaffold files use backticks for
+  // non-path content (config values, IPs, annotation keys) that produces
+  // false MISSING_PATH errors. See https://github.com/theDakshJaitly/mex/issues/79
+  const routerClaims = allClaims.filter((c) => basename(c.source) === "ROUTER.md");
+  const pathIssues = checkPaths(routerClaims, projectRoot, scaffoldRoot);
   allIssues.push(...pathIssues);
   checkerIssueCounts.push(["paths", pathIssues.length]);
 
diff --git a/test/public-api.test.ts b/test/public-api.test.ts
index 63f2e15..7f9b444 100644
--- a/test/public-api.test.ts
+++ b/test/public-api.test.ts
@@ -232,6 +232,52 @@ describe("public API — runDriftCheck", () => {
   });
 });
 
+describe("public API — runDriftCheck scopes checkPaths to ROUTER.md", () => {
+  it("does not produce MISSING_PATH issues from non-ROUTER.md files", async () => {
+    mkdirSync(join(tmpDir, ".mex/context"), { recursive: true });
+    writeFileSync(
+      join(tmpDir, ".mex/ROUTER.md"),
+      "---\nedges:\n  - target: context/architecture.md\n---\n# Router\n\nSee [architecture](context/architecture.md).\n",
+    );
+    // architecture.md has inline code that looks like paths but isn't real files
+    writeFileSync(
+      join(tmpDir, ".mex/context/architecture.md"),
+      "# Architecture\n\nUse `csi.kubeletRootDir: /var/lib/kubelet` and `192.168.5.0/24`.\n",
+    );
+    const report = await runDriftCheck(config);
+    const pathIssues = report.issues.filter((i) => i.code === "MISSING_PATH");
+    // These non-path inline codes should NOT produce MISSING_PATH errors
+    expect(pathIssues).toHaveLength(0);
+  });
+
+  it("still produces MISSING_PATH issues from ROUTER.md", async () => {
+    writeFileSync(
+      join(tmpDir, ".mex/ROUTER.md"),
+      "# Router\n\nSee `src/totally/missing.ts` for details.\n",
+    );
+    const report = await runDriftCheck(config);
+    const pathIssues = report.issues.filter((i) => i.code === "MISSING_PATH");
+    expect(pathIssues).toHaveLength(1);
+    expect(pathIssues[0].message).toContain("src/totally/missing.ts");
+  });
+
+  it("only flags ROUTER.md paths when both ROUTER.md and AGENTS.md have missing paths", async () => {
+    writeFileSync(
+      join(tmpDir, ".mex/ROUTER.md"),
+      "# Router\n\nSee `src/missing.ts`.\n",
+    );
+    writeFileSync(
+      join(tmpDir, ".mex/AGENTS.md"),
+      "# Agents\n\nSee `lib/also/missing.py`.\n",
+    );
+    const report = await runDriftCheck(config);
+    const pathIssues = report.issues.filter((i) => i.code === "MISSING_PATH");
+    // Only the ROUTER.md path should be flagged
+    expect(pathIssues).toHaveLength(1);
+    expect(pathIssues[0].message).toContain("src/missing.ts");
+  });
+});
+
 describe("public API — heartbeat", () => {
   it("checkHeartbeat returns the documented HeartbeatResult shape", () => {
     const result: HeartbeatResult = checkHeartbeat(config);