I've only seen something similar to this when cheaper programmers were got to replace me. I don't know exactly what they kept doing, but I think they had the notion that they needed to delete a db to disconnect it. That only affected one database, though.

Is something very privileged modifying database mysql? Check /var/lib/mysql (or wherever) to see if the databases are really gone or just inaccessible.

With DBI, the connect method usually specifies the database. You can change db with:

use DBI;
my ($user, $pass) = ('joe', 'joe');
my $dbh = DBI::connect('dbi:mysql:database=thisun',$user,$pass,{RaiseE
+rror=>1}) or die $!;
# now connected to thisun
$dbh->do('use thatun');
# now connected to thatun
[download]

Should be nothing there to wipe things out.

After Compline,
Zaxo