Sorry if I don’t understand, do you mean that the numbers on your invoices are not increasing in new documents?
If so, we are aware about this behavior, but this is not an issue coming from our plugin, but it seems to be related with a database configuration when the AUTO_INCREMENT attribute is not set.
As a workaround, you could try enabling the Calculate document numbers option, under WooCommerce > PDF Invoices > Advanced > Settings > Document Management & Behavior, to try to solve this issue: