Well, since you haven't gotten a better response, I'll say that I've never managed to get my non-printable keys in *anything* fixed the way I want except with flux and ice config files but screen has a ~/.screenrc file that allows you to bind keys. So that'd be what you wanted to look into, I guess. Though there's the usual nightmare of termcap and inputrc and even whether you've got your $TERM set right. My backspace works in screen so I'd guess you changed something that made it stop working since I never did anything to make mine work. So, no solution, but maybe some suggestions about places to look and things to try. If you'd like, I'll post up my ~/.screenrc though I don't know if it would work for you.
I think if I could ask for *anything* out of Linux it would be for all my keys to function in the same way in every app and to reflect my keyboard. And then to make it *easily and clearly* modifiable. And cut down on the 106 programs and config files that combine to mess up that one device. (That's a lot of things but it boils down to one: my keyboard is the I in IO - it'd better work.)