Hi,
I can understand your situation, but have to take the defensive route here: I won't be able to have a solution in place by midday tomorrow, and maybe not even until after the weekend. Sorry.
Exploring other options is the best idea for now, for your situation.
Using WP-Table Reloaded and TablePress together is possible, but needs some extra work. The first reason is that both plugins use the same WordPress Shortcode [table]. This can easily be circumvented, if you change the WP-Table Reloaded Shortcode with the help of the instructions at http://tobias.baethge.com/2010/01/extension-3-changing-the-table-shortcode/ You could change it to [wptrtable] for example.
The second reason is the CSS styling, which is slightly different in both plugins. Here, I recommend to deactivate the Default and Custom CSS in WP-Table Reloaded entirely, and to use the TablePress CSS for the tables from both plugins. This will also guarantee a uniform styling of your tables. To achieve that, just paste the lines
add_filter( 'wp_table_reloaded_table_css_class', 'wptr_add_tablepress_classes', 10, 2 );
function wptr_add_tablepress_classes( $classes, $table_id ) {
$classes[] = 'tablepress';
$classes[] = 'tablepress-id-' . $table_id;
return $classes;
}
to your functions.php (or actually to the Extension that changes the Shortcode, to keep everything together).
After that, all tables will have the TablePress styling.
Note that this is not really a long-term solution. as WP-Table Reloaded will be discontinued soo. Unless I'm able to find a solution to the actual issue in TablePress, you might need to look into a custom PHP/mySQL database solution. Unfortunately, I also don't know other table plugins that could handle your amount of tables (which is indeed more than the average user has).
Regards,
Tobias