diff --git a/.changeset/zesty-eagles-fly.md b/.changeset/zesty-eagles-fly.md
new file mode 100644
index 000000000..030b701f6
--- /dev/null
+++ b/.changeset/zesty-eagles-fly.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3565
+---
+**validate.health no longer warns W006 for not-started phases** - unchecked roadmap phase entries are treated as planned/future and no longer require on-disk phase directories until work has started. Fixes #3559.
diff --git a/sdk/src/query/validate.test.ts b/sdk/src/query/validate.test.ts
index 4f370f541..d63ba7001 100644
--- a/sdk/src/query/validate.test.ts
+++ b/sdk/src/query/validate.test.ts
@@ -643,6 +643,53 @@ describe('validateHealth', () => {
     expect(w006s.some(w => String(w.message).includes('Phase 7'))).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'), [
+      '# Roadmap',
+      '',
+      '## v1.1: Current',
+      '',
+      '- [x] **Phase 21: Active**',
+      '- [ ] **Phase 22: Future planned**',
+      '',
+      '### Phase 21: Active',
+      '',
+      '### Phase 22: Future planned',
+      '',
+    ].join('\n'));
+    await mkdir(join(tmpDir, '.planning', 'phases', '21-active'), { 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 w006s = warnings.filter(w => w.code === 'W006');
+    expect(w006s.some(w => String(w.message).includes('Phase 22'))).toBe(false);
+  });
+
+  it('does not alias 22A to 22 when suppressing W006 (#3565)', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), [
+      '# Roadmap',
+      '',
+      '## v1.1: Current',
+      '',
+      '- [x] **Phase 22: Started phase**',
+      '- [ ] **Phase 22A: Future variant**',
+      '',
+      '### Phase 22: Started phase',
+      '',
+      '### Phase 22A: Future variant',
+      '',
+    ].join('\n'));
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    const w006s = warnings.filter(w => w.code === 'W006');
+    expect(w006s.some(w => String(w.message).includes('Phase 22 in ROADMAP.md'))).toBe(true);
+  });
+
   it('does not emit I001 when plan file has descriptor but summary uses canonical stem (#3473)', async () => {
     await createHealthyPlanning();
     await mkdir(join(tmpDir, '.planning', 'phases', '68-bug-surface'), { recursive: true });
diff --git a/sdk/src/query/validate.ts b/sdk/src/query/validate.ts
index e68e072a8..dc48c5c67 100644
--- a/sdk/src/query/validate.ts
+++ b/sdk/src/query/validate.ts
@@ -594,9 +594,30 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
       const roadmapContent = await readFile(roadmapPath, 'utf-8');
       const roadmapPhases = new Set<string>();
       const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:/gi;
+      const phaseVariants = (phase: string): Set<string> => {
+        const variants = new Set<string>([phase]);
+        const dotIdx = phase.indexOf('.');
+        const head = dotIdx === -1 ? phase : phase.slice(0, dotIdx);
+        const tail = dotIdx === -1 ? '' : phase.slice(dotIdx);
+        const headMatch = head.match(/^(\d+)([A-Z]?)$/i);
+        if (!headMatch) return variants;
+        const numericHead = headMatch[1];
+        const letterSuffix = headMatch[2] || '';
+        variants.add(`${String(parseInt(numericHead, 10))}${letterSuffix}${tail}`);
+        variants.add(`${numericHead.padStart(2, '0')}${letterSuffix}${tail}`);
+        return variants;
+      };
+      const roadmapPhaseVariants = new Set<string>();
       let m: RegExpExecArray | null;
       while ((m = phasePattern.exec(roadmapContent)) !== null) {
         roadmapPhases.add(m[1]);
+        for (const variant of phaseVariants(m[1])) roadmapPhaseVariants.add(variant);
+      }
+      const notStartedPhases = new Set<string>();
+      const uncheckedPattern = /-\s*\[\s\]\s*\*{0,2}Phase\s+(\d+[A-Z]?(?:\.\d+)*)[:\s*]/gi;
+      let um: RegExpExecArray | null;
+      while ((um = uncheckedPattern.exec(roadmapContent)) !== null) {
+        for (const variant of phaseVariants(um[1])) notStartedPhases.add(variant);
       }
 
       const diskPhases = new Set<string>();
@@ -625,15 +646,18 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
       } catch { /* intentionally empty */ }
 
       for (const p of roadmapPhases) {
-        const padded = String(parseInt(p, 10)).padStart(2, '0');
-        if (!diskPhases.has(p) && !diskPhases.has(padded)) {
+        const variants = phaseVariants(p);
+        const existsOnDisk = [...variants].some((variant) => diskPhases.has(variant));
+        const isNotStarted = [...variants].some((variant) => notStartedPhases.has(variant));
+        if (!existsOnDisk) {
+          if (isNotStarted) continue;
           addIssue('warning', 'W006', `Phase ${p} in ROADMAP.md but no directory on disk`, 'Create phase directory or remove from roadmap');
         }
       }
 
       for (const p of diskPhases) {
-        const unpadded = String(parseInt(p, 10));
-        if (!roadmapPhases.has(p) && !roadmapPhases.has(unpadded)) {
+        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');
         }
       }