To answer your question: When an application is received, it is opened by an AECO who is observed by another AECO acting as a witness. The two people eyeball the contents and record it into the proviso system, one calls out the contents item by item, and the other one books it into the system. Totally British.
Each day, the system prints out a list of which applications are pending, who has them, where they are, what the issues are, and so on. The ECM takes the list and chases the exceptions. If an application goes missing, there's a lock-down until its found. Other times, if the ECM decides an app is going to be exceptional, they will notify you.
The system does not leave much room for stuff to fall through the cracks. Obviously so because it's the business they are in. I have never had a case where an app went missing, and have never HEARD of a case where an app went missing. They are pretty good at that part. Also why Vicky and I and others are not so fussed.
The notification email is a courtesy, not part of the procedure, but they are pretty good about it. Did you check, double check, and triple check that your email was written correctly? Was it totally legible? No numbers that could be mistaken for letters and all that? All the basic checks. Spam filter and so on.
If it wasn't DHS and wasn't a *bleep*-up somewhere, and they have good contact details for you, then you're fine. If they misplaced the app, it will flag up in proviso as an exception. If it never reached them, the delivery service would not have sent a confirm.