When you install Xoops you choose a username and password that is used to create the database etc. The password is encrypted and placed into mainfile.php. If I want to change the password how do I generate a new encrypted password so that I can edit mainfile.php and replace it it? This is something I might want to do on a regular basis to increase site security.

If you are referring to the site's database password: You can change this at any time by editing mainfile.php, BUT you must also change (or add the new password) to the site's database access on the server to match this. Failure to match passwords will stop the site connecting and result in an error page.

Always return the mainfile.php back to chmod 0444 to maintain minimal access.