diff --git a/.changeset/sturdy-wolves-glide.md b/.changeset/sturdy-wolves-glide.md
new file mode 100644
index 000000000..b8ba26567
--- /dev/null
+++ b/.changeset/sturdy-wolves-glide.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3564
+---
+**validate.health no longer raises W007 for archived milestone phases** - archived `v*-phases` directories remain valid for historical W006 checks, but W007 now only reports unexpected active phase directories. Fixes #3560.
diff --git a/sdk/src/query/validate.test.ts b/sdk/src/query/validate.test.ts
index d63ba7001..06ca231d2 100644
--- a/sdk/src/query/validate.test.ts
+++ b/sdk/src/query/validate.test.ts
@@ -643,6 +643,26 @@ describe('validateHealth', () => {
     expect(w006s.some(w => String(w.message).includes('Phase 7'))).toBe(false);
   });
 
+  it('does not emit W007 for archived milestone-only phase dirs (#3560)', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), [
+      '# Roadmap',
+      '',
+      '## v1.1: Current',
+      '',
+      '### Phase 21: Active',
+      '',
+    ].join('\n'));
+    await mkdir(join(tmpDir, '.planning', 'phases', '21-active'), { recursive: true });
+    await mkdir(join(tmpDir, '.planning', 'milestones', 'v1.0-phases', '02-old-shipped-phase'), { recursive: true });
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    const w007s = warnings.filter(w => w.code === 'W007');
+    expect(w007s.some(w => String(w.message).includes('Phase 02'))).toBe(false);
+  });
+
   it('does not emit W006 for unchecked future phases with no directory (#3559)', async () => {
     await createHealthyPlanning();
     await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), [
diff --git a/sdk/src/query/validate.ts b/sdk/src/query/validate.ts
index dc48c5c67..1a0fe4a17 100644
--- a/sdk/src/query/validate.ts
+++ b/sdk/src/query/validate.ts
@@ -621,12 +621,16 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
       }
 
       const diskPhases = new Set<string>();
+      const activeDiskPhases = new Set<string>();
       try {
         const entries = await readdir(phasesDir, { withFileTypes: true });
         for (const e of entries) {
           if (e.isDirectory()) {
             const dm = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
-            if (dm) diskPhases.add(dm[1]);
+            if (dm) {
+              diskPhases.add(dm[1]);
+              activeDiskPhases.add(dm[1]);
+            }
           }
         }
       } catch { /* intentionally empty */ }
@@ -655,7 +659,7 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
         }
       }
 
-      for (const p of diskPhases) {
+      for (const p of activeDiskPhases) {
         const variants = phaseVariants(p);
         if (![...variants].some((variant) => roadmapPhaseVariants.has(variant))) {
           addIssue('warning', 'W007', `Phase ${p} exists on disk but not in ROADMAP.md`, 'Add to roadmap or remove directory');