There is Hope!
Hello JK,
Recently me and my two family members travelled from KHI-LON on Emirates. On return I thought I'll have our miles credited to our account.
All I did was call the Emirates office in Khi and gave them my Skywards number and our E-ticket number. I was also told that with an E-ticket, if there are any missing miles there is no need for Boarding passes even though I had saved them for the day. I was given a confirmation on the phone for all 3 pax that the miles have been credited. I checked online 5 minutes later and there were posted!
So you may be in luck if you had an E-ticket.
I've noticed that not all agents know this so while you're on the phone tell them that you have an E-ticket and that you don't see why you need the boarding stubs. It may work and the agent may learn something new!
Good Luck!