diff --git a/init.sh b/init.sh
index 7e59bc0..35a4137 100755
--- a/init.sh
+++ b/init.sh
@@ -737,7 +737,12 @@ setupConfigsFromRepo()
 
     sudo mkdir -p "$dst"
 
-    if ! sudo cp -a "$src"/. "$dst"/; then
+    # No-clobber: only seed config files that don't already exist. On a fresh
+    # install this copies the whole template; on a re-run/deploy it preserves the
+    # user's live values (a plain cp -a here silently reset e.g. the Docker
+    # install type back to the template default). New *keys* in existing files
+    # are added separately by the add-only reconcile pass.
+    if ! sudo cp -an "$src"/. "$dst"/; then
         isError "Failed to copy configs from $src to $dst — aborting."
         exit 1
     fi
@@ -1047,7 +1052,8 @@ sync_configs_from_install() {
 		return 1
 	fi
 	sudo mkdir -p "$dst"
-	if ! sudo cp -a "$src"/. "$dst"/; then
+	# No-clobber: preserve the user's live config values; only add new files.
+	if ! sudo cp -an "$src"/. "$dst"/; then
 		echo "ERROR: Failed to sync configs from $src to $dst."
 		return 1
 	fi