From the Woo forums:
We have a limit of 50 linked variations per product right now (to
prevent memory issues), anything above that is considered to be very
complex and in need of some custom work. It is not easy to manage a
single product with over 3000 variations, in no eCommerce software out
there.
That said, looks like you have to hack the plugin code or create an action hook (not sure how to, but it is supported by the plugin in this function case) to modify the behavior of the function woocommerce_link_all_variations.
Max 100 is an original comment in the file.
/*
* File: /plugins/woocommerce/woocommerce-ajax.php
* Line: 487
* WooCommerce: v1.5.6
*/
// Max 100
if ($added>49) break;