Sorry to hear about what happened to you, however let me tell you that this is not something unusual with IRCC. My wife received a PFL regarding our marriage certificate, and we uploaded all supporting documents well within the deadline. And, guess what? Her application was rejected because "they never received anything". We had to reapply with the exact same documents, and her application was approved within a month.
You can try to ask them reopen your case, or even contact your local MP, but I wouldn't get my hopes up after going through the same stress before. It's pathetic that they don't even listen to us or assist us in these instances.
******* IRCC Magic *******