diff --git a/tools-sync/scripts/sync_repos.ps1 b/tools-sync/scripts/sync_repos.ps1
index c548545..19968cc 100644
--- a/tools-sync/scripts/sync_repos.ps1
+++ b/tools-sync/scripts/sync_repos.ps1
@@ -117,6 +117,28 @@ function Get-DirFingerprint([string]$Path) {
     return (($lines | Sort-Object) -join "`n")
 }
 
+# Agent tools each keep their own skills directory and a host installer may pick any one of them
+# as a skill's physical home, linking the rest at it. Finding those linkers is how we tell a
+# host-installed skill from one authored on the Codex side.
+function Get-SkillDirLinkers([string]$TargetPath) {
+    $roots = @()
+    foreach ($d in Get-ChildItem $env:USERPROFILE -Directory -Force -ErrorAction SilentlyContinue |
+                   Where-Object { $_.Name -like ".*" }) {
+        foreach ($sub in @("skills", "agent\skills")) {
+            $cand = Join-Path $d.FullName $sub
+            if (Test-Path $cand) { $roots += $cand }
+        }
+    }
+    $hits = @()
+    foreach ($r in $roots) {
+        if (Test-UnderPath $TargetPath $r) { continue }   # the home itself
+        $link = Join-Path $r (Split-Path $TargetPath -Leaf)
+        $item = Get-Item -LiteralPath $link -Force -ErrorAction SilentlyContinue
+        if ($item -and (Test-IsLink $item) -and ((Get-LinkTarget $item) -eq $TargetPath)) { $hits += $r }
+    }
+    return $hits
+}
+
 function New-SkillJunction([string]$LinkPath, [string]$TargetPath, [string]$Why) {
     if ($DryRun) { Write-Host "  (dry-run) would link $LinkPath -> $TargetPath  [$Why]"; return }
     New-Item -ItemType Junction -Path $LinkPath -Target $TargetPath | Out-Null
@@ -272,6 +294,17 @@ foreach ($reg in $registries) {
         $name = Split-Path $copyPath -Leaf
         $primaryPath = Join-Path $ClaudeSkills $name
         if (-not (Test-Path $copyPath)) { continue }   # already resolved earlier this run
+
+        # The primary entry is itself a link into a registry: this skill's physical home is the
+        # registry, and the host installed it that way round (Orca does exactly this - it puts the
+        # real directory in ~\.agents\skills and links every tool at it). Collapsing the registry
+        # copy here would point the link at itself and DELETE the only copy. Leave it to its owner.
+        $primaryItem = Get-Item -LiteralPath $primaryPath -Force -ErrorAction SilentlyContinue
+        if ($primaryItem -and (Test-IsLink $primaryItem)) {
+            $foreign++
+            continue
+        }
+
         $repairLinks += $copyPath
 
         # --- real directory holding a skill ---
@@ -287,6 +320,15 @@ foreach ($reg in $registries) {
                 Write-Host "  registry-only skill NOT ingested (-NoIngest): $name"
                 continue
             }
+            # Other agent tools linking at this directory mean it is a host-installed skill's
+            # physical home, not a skill authored here. Moving it inverts the host's layout and
+            # its own updater then fights us for the location.
+            $linkers = Get-SkillDirLinkers $copyPath
+            if ($linkers) {
+                $script:Notes += "$name lives in $copyPath and $($linkers.Count) other tool registr$(if ($linkers.Count -eq 1) { 'y links' } else { 'ies link' }) at it; treated as host-installed and left alone."
+                Write-Host "  host-installed skill (linked from $($linkers.Count) other tool(s)), not ingested: $name"
+                continue
+            }
             Write-Host "  INGEST registry-only skill: $name  ($copyPath -> $primaryPath)"
             if (-not $DryRun) { Move-Item -LiteralPath $copyPath -Destination $primaryPath }
             $script:Ingested += $name
@@ -332,7 +374,10 @@ if ($MirrorRegistry) {
         if (-not $DryRun) { Remove-Item -Recurse -Force $mirrorGit }
     }
 
-    $primarySkills = Get-ChildItem $ClaudeSkills -Directory | Where-Object { $_.Name -notlike ".*" }
+    # A primary entry that is itself a link belongs to whichever host installed it (its real home
+    # is a registry the host already exposes to Codex). Mirroring it would register it twice.
+    $primarySkills = Get-ChildItem $ClaudeSkills -Directory -Force |
+        Where-Object { $_.Name -notlike ".*" -and -not (Test-IsLink $_) }
     foreach ($d in $primarySkills) {
         $link = Join-Path $MirrorRegistry $d.Name
         if (Test-Path $link) { continue }
diff --git a/tools-sync/tests/test_sync_repos_registries.ps1 b/tools-sync/tests/test_sync_repos_registries.ps1
index 05bb385..a8f1e66 100644
--- a/tools-sync/tests/test_sync_repos_registries.ps1
+++ b/tools-sync/tests/test_sync_repos_registries.ps1
@@ -27,6 +27,12 @@ try {
     # A link into the other registry rather than the primary: the drift case.
     New-Item -ItemType Junction -Path (Join-Path $codex "shared") -Target (Join-Path $agents "shared") | Out-Null
 
+    # Host-installed shape: the real directory lives in a registry and the PRIMARY is the link
+    # (Orca installs this way). Collapsing the registry copy here would make the link point at
+    # itself and delete the only copy - the reconciler must recognise it and keep its hands off.
+    New-Skill (Join-Path $agents "hostowned") "installed by the host"
+    New-Item -ItemType Junction -Path (Join-Path $primary "hostowned") -Target (Join-Path $agents "hostowned") | Out-Null
+
     # A local bare repo stands in for origin so Phase 1 completes and Phase 2 actually runs.
     $origin = Join-Path $root "origin.git"
     & git init --quiet --bare $origin
@@ -57,6 +63,15 @@ try {
     if ((Get-Content -Raw (Join-Path $primary "forked\SKILL.md")) -notmatch 'primary body') { throw "primary was overwritten by a conflict`n$output" }
 
     if ($output -notmatch 'not a skill dir') { throw "directory without SKILL.md not reported`n$output" }
+
+    # The host-installed skill must survive intact, with the primary still a link at the registry.
+    $hostReal = Get-Item -Force (Join-Path $agents "hostowned")
+    if ($hostReal.LinkType -eq "Junction") { throw "host-installed skill's real dir was collapsed into a link`n$output" }
+    if ((Get-Content -Raw (Join-Path $agents "hostowned\SKILL.md")) -notmatch 'installed by the host') { throw "host-installed skill's content was lost`n$output" }
+    $hostPrimary = Get-Item -Force (Join-Path $primary "hostowned")
+    if (($hostPrimary.Target | Select-Object -First 1) -ne (Join-Path $agents "hostowned")) { throw "primary link to the host-installed skill was repointed`n$output" }
+    # Mirroring it into the registry Codex scans would register the same skill twice.
+    if (Test-Path (Join-Path $codex "hostowned")) { throw "host-installed skill was mirrored, double-registering it`n$output" }
     # Mirror registry must expose every primary skill, including the freshly ingested one.
     foreach ($name in @("shared", "forked", "codexborn")) {
         if (-not (Test-Path (Join-Path $codex "$name\SKILL.md"))) { throw "mirror missing $name`n$output" }