diff --git a/cli/src/services/install-service.ts b/cli/src/services/install-service.ts
index 33fff91c..d1ade76e 100644
--- a/cli/src/services/install-service.ts
+++ b/cli/src/services/install-service.ts
@@ -29,6 +29,7 @@ export interface InstallOptions {
   resolved?: ResolveResponse | undefined
   expectedTargetFiles?: Record<string, Record<string, string>> | undefined
   allowTargetDrift?: boolean | undefined
+  requireExistingTargets?: boolean | undefined
 }
 
 interface StagedInstall {
@@ -137,15 +138,23 @@ export async function installSkill(options: InstallOptions): Promise<{ installed
       }, resolved)
 
       for (const item of staged) {
-        if (await pathExists(item.skillDir)) {
+        const targetExists = await pathExists(item.skillDir)
+        if (!targetExists && options.requireExistingTargets) {
+          throw new CliError(`installed target disappeared before upgrade commit: ${item.skillDir}`, EXIT.validation, {
+            path: item.skillDir,
+            next: 'reinstall the Skill explicitly before upgrading it'
+          })
+        }
+        if (targetExists) {
           if (!options.force) {
             throw new CliError(`skill already installed at ${item.skillDir}`, EXIT.filesystem, {
               path: item.skillDir,
               next: 'pass --force to overwrite'
             })
           }
-          item.backupDir = `${item.skillDir}.skillhub-backup-${process.pid}-${Date.now()}`
-          await rename(item.skillDir, item.backupDir)
+          const backupDir = `${item.skillDir}.skillhub-backup-${process.pid}-${Date.now()}`
+          await rename(item.skillDir, backupDir)
+          item.backupDir = backupDir
           await assertReplaceableInstallation(item.backupDir, item.skillDir, {
             registry: options.registry,
             namespace: options.namespace,
diff --git a/cli/src/services/upgrade-service.ts b/cli/src/services/upgrade-service.ts
index ab574f90..d693bc51 100644
--- a/cli/src/services/upgrade-service.ts
+++ b/cli/src/services/upgrade-service.ts
@@ -231,7 +231,8 @@ export async function executeSkillUpgradePlan(
       force: true,
       home: options.home,
       expectedTargetFiles: item.expectedTargetFiles,
-      allowTargetDrift: item.allowTargetDrift
+      allowTargetDrift: item.allowTargetDrift,
+      requireExistingTargets: true
     })
   }
 }
diff --git a/cli/test/integration/upgrade-command.test.ts b/cli/test/integration/upgrade-command.test.ts
index c8863b39..07413753 100644
--- a/cli/test/integration/upgrade-command.test.ts
+++ b/cli/test/integration/upgrade-command.test.ts
@@ -1,4 +1,4 @@
-import { mkdir, readFile, writeFile } from 'node:fs/promises'
+import { access, mkdir, readFile, rm, writeFile } from 'node:fs/promises'
 import { join } from 'node:path'
 import { afterEach, describe, expect, test } from 'bun:test'
 import { strToU8, zipSync } from 'fflate'
@@ -18,6 +18,15 @@ function makeSkillZip(content: string): Uint8Array {
   return zipSync({ 'SKILL.md': strToU8(content) })
 }
 
+async function exists(path: string): Promise<boolean> {
+  try {
+    await access(path)
+    return true
+  } catch {
+    return false
+  }
+}
+
 describe('upgrade command', () => {
   test('check is side-effect free and execute upgrades an installed skill', async () => {
     const env = await createTempHome()
@@ -166,6 +175,47 @@ describe('upgrade command', () => {
     expect(inventory.items[0]).toMatchObject({ version: '1.0.0', fingerprint: 'fp-v1' })
   })
 
+  test('a target removed after planning is not recreated by upgrade', async () => {
+    const env = await createTempHome()
+    const skill = {
+      namespace: 'global',
+      slug: 'removed-late',
+      version: '1.0.0',
+      versionId: 1,
+      fingerprint: 'fp-v1',
+      zipBytes: makeSkillZip('# v1')
+    }
+    const registry = await startFakeRegistry({ skills: [skill] })
+    registries.push(registry)
+    const rootDir = join(env.cwd, 'skills')
+    await mkdir(rootDir, { recursive: true })
+    await runCli(['install', '@global/removed-late', '--dir', rootDir, '--registry', registry.url], {
+      HOME: env.home,
+      USERPROFILE: env.home
+    }, { cwd: env.cwd })
+
+    skill.version = '1.1.0'
+    skill.versionId = 2
+    skill.fingerprint = 'fp-v2'
+    skill.zipBytes = makeSkillZip('# v2')
+    const tokenForRegistry = async () => undefined
+    const plan = await planSkillUpgrades({
+      coordinates: ['@global/removed-late'],
+      registry: registry.url,
+      force: false,
+      home: env.home,
+      tokenForRegistry
+    })
+    const skillDir = join(rootDir, 'removed-late')
+    await rm(skillDir, { recursive: true })
+
+    await expect(executeSkillUpgradePlan(plan, { home: env.home, tokenForRegistry }))
+      .rejects.toThrow('installed target disappeared before upgrade commit')
+    expect(await exists(skillDir)).toBe(false)
+    const inventory = JSON.parse(await readFile(join(env.home, '.skillhub', 'inventory.json'), 'utf-8'))
+    expect(inventory.items[0]).toMatchObject({ version: '1.0.0', fingerprint: 'fp-v1' })
+  })
+
   test('new installs persist absolute targets and legacy relative targets are blocked safely', async () => {
     const env = await createTempHome()
     const skill = {