I have been using the patch ( http://bugs.debian.org/cgi-bin/bugreport.cgi?msg=25;filename=0001-If-mtime-of-existing-debfile-changed-update-databas.patch;att=1;bug=463260 )with apt 0.6.46.4-0.1 ('etch') to no ill effect for several weeks. It has fixed my issues with duplicate version uploads. Upstream, please commit this!
Thanks -joey