[Zandig]

Looked into this a bit further inside the eqemu_server.pl file, at this particular section:

sub database_dump_player_tables
{
    check_for_database_dump_script();
    print "[Database] Performing database backup of player tables....\n";
    get_remote_file($eqemu_repository_request_url . "utils/sql/character_table_list.txt",
        "backups/character_table_list.txt");

    $tables = "";
    open(FILE, "backups/character_table_list.txt");
    $i = 0;
    while (<FILE>) {
        chomp;
        $o      = $_;
        $tables .= $o . ",";
    }
    $tables = substr($tables, 0, -1);

    print `perl database_dumper.pl database="$db" loc="backups" tables="$tables" backup_name="player_tables_export" nolock`;

    print "[Database] Press any key to continue...\n";

The file "character_table_list.txt" is not being found or is empty at the URL:
"https://raw.githubusercontent.com/EQEmu/Server/master/utils/sql/character_table_list.txt"
and is therefore creating an empty file which in turn backs up the entire database.

The solution for now is to back up your player tables manually until the character_table_list.txt file is available.