When I go to the server area of global configuration- which is where I assume the jos_ prefix would need to be changed, I see:
WARNING! Do not change unless you have a database built using tables with the prefix you are setting.

I don't have a database built with different values, and have no idea how to change this without breaking the entire install.

I have actually read most of the documentation, and understand that this needs to be changed, yet not a word on how to change it.

What do I do?

When you use the Joomla Installation and you arrive the the database page where you can specify the server, db name, user and password you have to open the advanced setting pannel to have access to the table prefix.
See the "demo installation" document that show you that.

When you create a new slave site with JMS with it replication, you just have to give the new table prefix and JMS will do the job for you like you had to do with the "advanced setting" panel of Joomla.

I have a similar probem. At the time of installation I did not change the jos_ prefix to master_ as I was supposed to.

Is it possible to go back now and make the replacement without incident?

NO, in Joomla, there is no method to rename the jos_ into master_.
You can either use a PHPMyAdmin tool or similar to perform the MySQL rename table;
OR you can use JMS replication mechanism to duplicate the jos_ tables into master_. When the replication is performed, you could delete the jos_.
It this is freesh installation (as I suppose), this is faster to re-do it.

The PHP Admin Tool did the trick - allowed me to go back and rename all of the files with jos_ to master_ I then went into the configuration file and replaced jos_ with master_ and everything works!!

I had the same problem, and fixed it using the following sql statement inside the php admin:


You have to do this for every table name in the database. Then open the configuration.php file, and change the prefix from jos_ to master_.