diff --git a/plugin/src/Reconciler/diff.lua b/plugin/src/Reconciler/diff.lua
index bb3409f2..175407fc 100644
--- a/plugin/src/Reconciler/diff.lua
+++ b/plugin/src/Reconciler/diff.lua
@@ -35,17 +35,18 @@ local SCRIPT_CLASS_NAMES = {
 }
 
 local function shouldDeleteChild(virtualInstance, childInstance)
-	if shouldDeleteUnknownInstances(virtualInstance) then
-		return true
-	end
-
 	-- When the parent has glob-ignored children, suppress ALL deletions
-	-- (including scripts). This differs from scripts-only mode where
-	-- scripts are still eligible for deletion.
+	-- (including scripts) unconditionally. This must be checked before
+	-- shouldDeleteUnknownInstances because project nodes and meta files
+	-- can override ignoreUnknownInstances independently.
 	if virtualInstance.Metadata and virtualInstance.Metadata.globIgnoredChildren then
 		return false
 	end
 
+	if shouldDeleteUnknownInstances(virtualInstance) then
+		return true
+	end
+
 	-- In scripts-only mode (where parent has ignoreUnknownInstances: true),
 	-- we still want to allow deletion of scripts. This ensures deleted
 	-- script files show up in the sync diff.