It wont break DA if done right but can break DA if some steps are mixed. By default mysql uses a different db dir to the one DA set's so if this isn't specified then your current db's would stop functioning, the other potential issue is that every min DA checks for dead processes and if mysqld is down it runs /usr/local/etc/rc.d/mysqld which points to the DA installed mysql so I renamed that file and copied /usr/local/etc/rc.d/mysql-server.sh to it and that will make DA run the ports version instead, with these 2 points addressed you should have no issues at all. My DA has been functioning fine for weeks like this. As a bonus it makes upgrading mysql a doddle since doing it via the ports is much simpler.