diff --git a/tools-sync/scripts/sync_repos.ps1 b/tools-sync/scripts/sync_repos.ps1
index f96b575..a5ee386 100644
--- a/tools-sync/scripts/sync_repos.ps1
+++ b/tools-sync/scripts/sync_repos.ps1
@@ -73,7 +73,9 @@ if (-not (Test-Path $CodexSkills)) { New-Item -ItemType Directory -Force $CodexS
 # origin/main ever arrived (init succeeded, fetch didn't).
 $needBootstrap = -not (Test-Path (Join-Path $CodexSkills ".git"))
 if (-not $needBootstrap) {
-    $r = Invoke-Git $CodexSkills @("rev-parse", "--verify", "--quiet", "refs/remotes/origin/$Branch")
+    # Upstream config is written as the very last bootstrap step, so its absence
+    # means a previous bootstrap died partway — redo it (all steps are idempotent).
+    $r = Invoke-Git $CodexSkills @("config", "--get", "branch.$Branch.merge")
     if ($r.Code -ne 0) { $needBootstrap = $true }
 }
 
@@ -82,6 +84,7 @@ if ($needBootstrap) {
     if ($DryRun) { Write-Host "(dry-run) would git init + fetch + align to origin/$Branch"; exit 0 }
     Invoke-Git $CodexSkills @("init") | Out-Null
     Invoke-Git $CodexSkills @("remote", "add", "origin", $RepoUrl) | Out-Null
+    Invoke-Git $CodexSkills @("remote", "set-url", "origin", $RepoUrl) | Out-Null
     $r = Invoke-Git $CodexSkills @("fetch", "origin", $Branch)
     if ($r.Code -ne 0) {
         # Flaky server on a full first fetch is common; the primary checkout already
@@ -95,7 +98,9 @@ if ($needBootstrap) {
     Invoke-Git $CodexSkills @("branch", "-f", $Branch, "origin/$Branch") | Out-Null
     Invoke-Git $CodexSkills @("checkout", $Branch) 2>$null | Out-Null
     $drift = Invoke-Git $CodexSkills @("status", "--porcelain")
-    $modified = ($drift.Out -split "`n" | Where-Object { $_ -match '^\s*(M|D)' })
+    # Only M is real local drift worth rescuing; D just means the file hasn't been
+    # materialized in this checkout yet, so overwriting loses nothing.
+    $modified = ($drift.Out -split "`n" | Where-Object { $_ -match '^\s*M' })
     if ($modified -and -not $Force) {
         Write-Host "these tracked files differ locally from the repo:"
         $modified | ForEach-Object { Write-Host "  $_" }