Ensure that pruned Instances aren't treated as existing in syncback (#1179)

Closes #1178.

rojo-test/syncback-tests/ref_properties_pruned/input-project/default.project.json

@@ -0,0 +1,9 @@
+{
+  "name": "ref_properties_pruned",
+  "tree": {
+    "$className": "DataModel",
+    "ServerScriptService": {
+      "$path": "src"
+    }
+  }
+}