yes, thats why you have to set up the protected slots.
i just seen some dude the other day lvl 90 , had some really good raid gear... switched to pvp blues... then started bot to go farm herbs... and guess what... his raid gear is gone now.
by default the bot will not sell things that are soul-bound to you, however if your using Dungeonbuddy it is designed to get rid of unneeded gear so if not setup correctly it could sell off that gear.