Wait and see if the embassy ask you to go to an inteview and provide info the courier told you wasn't meant to go in the bag! Then make a loud and official compaint about it.
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we didn't really take their advice and made sure almost everything we had went in the envelope anyway. The only thing i changed was to cut down the amount of chat transcripts, just mabye 1 page for each time we were online, then wrote in big letters on the front page "75% OF CHAT TRANSCRIPTS REMOVED BY TT SERVICES AS NOT REQUIRED".