Allow active licenses to get updates if they're not at the limit, no matter what.

edd-auto-activate-sites.php

<?php
/**
 * Allow active licenses to get updates if they're not at the limit, no matter what.
 *
 * @param bool $is_active         Whether the site is active or not.
 * @param int  $license_id        The license ID.
 * @param string $passed_site_url The site URL.
 *
 * @return bool Whether the site is active or not.
 */
function wpf_is_site_active_auto_activate_site( $is_active = false, $license_id = 0, $passed_site_url = '' ) {

	if ( true === $is_active ) {
		return true; // Already passed the check.
	}

	$license = edd_software_licensing()->get_license( $license_id );

	// Only allow active licenses to get updates if they're not at the limit.
	if ( ! $license || $license->is_at_limit() || 'active' !== $license->status ) {
		return $is_active;
	}

	$site = trailingslashit( edd_software_licensing()->clean_site_url( $passed_site_url ) );

	$args = array(
		'site_name'  => $site,
		'license_id' => $license_id,
		'activated'  => 0,
		'fields'     => 'site_id',
	);

	$exists = edd_software_licensing()->activations_db->get_activations( $args );

	if ( $exists ) {
		// If the site has already been deactivated, don't re-activate it.
		return $is_active;
	}

	// And then add the site.
	$license->add_site( $passed_site_url );

	// And enter this activation in the log.
	edd_software_licensing()->log_license_activation( $license->ID, $_SERVER );

	return true;
}

add_filter( 'edd_sl_is_site_active', 'wpf_is_site_active_auto_activate_site', 10, 3 );