In your post, the letter states,
“As your application does not meet the requirements of R 10 of IRPA, it is considered incomplete and is being returned to you along with your processing fee. A copy of your application has not been retained.”
You have to reapply from scratch (unless you have other instructions) and not just upload a new WES document. From the first application, your letters states that your processing fee will be refunded (takes several weeks) because your application was closed. Because you are submitting a new application, you pay fees. Did you submit a brand new application because that it was you must do and not just upload the WES document? Did you get the proper WES report in only a couple of days?