Hmm, for what it’s worth, I don’t experience this issue. When I enable User Agent banning inside BWP it seems to add to the top of .htaccess and it pushes my old stuff down. In other words, nothing is over-written.
I also want to chime in on this issue. I would love to see some improvements made with the User Agent ban feature. I don’t want to hi-jack this thread with specifics, but I am sure many other users would appreciate improvements in this area. I would be willing to pay for it, in fact.