edd_pre_add_to_cart.php

<?php

/***
Allow a product to be added only once to cart
***/

function drw_edd_one_item_checkout( $download_id, $options ) {
	
	if ( edd_item_in_cart($download_id) ) {
					
		$cart_contents = edd_get_cart_contents();
		$cart_ids = array();

		foreach( $cart_contents as $item) {
      			$cart_ids[] = $item['id'];
		}
		
		$cart_key = array_search ($download_id, $cart_ids);
		
		edd_remove_from_cart( $cart_key);
		
		set_query_var( 'edd_duplicate', 'duplicate' );
	}				
}

add_action( 'edd_pre_add_to_cart', 'drw_edd_one_item_checkout', 10, 2 );

/***
Set warning if duplicate is set
***/

function drw_edd_checkout_warnings() {

  if ( get_query_var('edd_duplicate') ) {

    printf('<div class="alert">%s</div>', __('This item can only be purchased once', 'drw'));

  }
}

add_action( 'edd_before_checkout_cart', 'drw_edd_checkout_warnings' );