Hmmn... I guess the short answer is be careful and not screw up the database :) To be honest though, it sounds very strange to me that all the databases got deleted, I doubt that is something you can do accidently.

You can use the GRANT statement in MySQL (see docs) to create a user that has limited SELECT/INSERT/DELETE permissions. This saves you from dropping tables etc by mistake. This is a good idea anyway, from a security standpoint.

While you could use DBD::Multiplex to use 2 different databases a much better (and much simpler) solution would just be to have a cron job to back up your database on a regular (nightly, even hourly) basis.

gav^