Use the woocommerce filter i.e woocommerce_get_sku to modify the SKU.
add_filter( 'woocommerce_get_sku', 'wp_8665_woocommerce_get_sku', 10, 2 );
function wp_8665_woocommerce_get_sku( $sku, $product ) {
if ( ! is_admin() ) {
$parts = explode( '.', $sku );
// Only first two parts
$parts = array_slice( $parts, 0, 2 );
// OR all parts except last (remove above)
// array_pop( $parts );
$sku = implode( '.', $parts );
}
return $sku;
}