If you're flying on the airline for your program and the ticket has your FF number on it, you're almost without exception safe. You got the upgrade consideration based on that number, so no worries. When you fly a code share with the same number on there you are generally fine. The only place I run into issues is with Alaska when my FF number won't go on the ticket or it's an actual American flight. In those cases, I always keep my boarding pass.

I'd suggest that as a best practice you get in the habit of putting your pass somewhere in your luggage, wallet, purse, what have you and throwing it away when you see the miles post. That's the only real way to make sure you'll get the miles. The reason for this is that is the only way to show that you actually used this program and not another program for the flight. You can get the airlines to ignore this is special circumstances, but in general they want to see the boarding pass.