Following workaround should work:
In case you don't need the product manufacturer or product model fields, use one of those to set a special flag. Like a manufacturer called "ShopAandB".
For the 2nd store where you only display 50 of those product just perform a simple flagcheck in the file tpl_product_info_display.php:
if ($products_model == "ShopAandB") {
// display product
} else {
// do not display
}
Using that method you could use the same DB, just make sure you use the same mods like stock by attributes etc, otherwise it will mess up the database.
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