Yeah, I also have one that fixes the prompt to the top so you only see a small '$' at the current line, but it messes up the terminal history.
However, for your problem, have you considered the terminal's title instead of the top line of the tty? printf '\033]0;foo\007'
Edit: If I understand what you're doing, then maybe you can use this:
tput ind; tput home; tput il1; echo -n "header"; tput el; tput cup $LINES 0
Use "man terminfo" to lookup things like "il1" and use "infocmp" to see what they translate to in your terminal.