...from my archives...
The Hypertech will do everything needed for rear axle ratio changes.... except for... the altering of the TCC Slip Table. And because of this, a C5 A4 with a non factory rear axle ratio will eventually set the P1870 error code and place the tranny into the limp mode.
The Hypertech has this "bug"... and as far as I know - it was never corrected.
more gear swap info here:
http://mikemercury.home.att.net/342.htm