I have implemented some changes that seem to resolve the issue but if anyone can look over this and feedback that would be great.
vendor/magento/framework/Session/SessionManager.php

public function regenerateId()
    {
        if (headers_sent()) {
            return $this;
        }

        if ($this->isSessionExists()) {
            $oldSessionId = session_id();            
            session_regenerate_id();   //regen the session
            $new_session_id = session_id();

            $_SESSION['new_session_id'] = $new_session_id;

            // Set destroy timestamp
            $_SESSION['destroyed'] = time();

            // Write and close current session;
            session_commit();
            $oldSession = $_SESSION;   //called after destroy - see destroy!
            // Start session with new session ID
            session_id($new_session_id);
            ini_set('session.use_strict_mode', 0);
            session_start();
            ini_set('session.use_strict_mode', 1);
            $_SESSION = $oldSession;
            // New session does not need them
            unset($_SESSION['destroyed']);
            unset($_SESSION['new_session_id']);  
        } else {
            session_start();
        }
        $this->storage->init(isset($_SESSION) ? $_SESSION : []);

        if ($this->sessionConfig->getUseCookies()) {
            $this->clearSubDomainSessionCookie();
        }
        return $this;
    }

and also the start function needs replacing with this

public function start()
    {
        if (!$this->isSessionExists()) {
            \Magento\Framework\Profiler::start('session_start');

            try {
                $this->appState->getAreaCode();
            } catch (\Magento\Framework\Exception\LocalizedException $e) {
                throw new \Magento\Framework\Exception\SessionException(
                    new \Magento\Framework\Phrase(
                        'Area code not set: Area code must be set before starting a session.'
                    ),
                    $e
                );
            }

            // Need to apply the config options so they can be ready by session_start
            $this->initIniOptions();
            $this->registerSaveHandler();
            if (isset($_SESSION['new_session_id'])) {
             // Not fully expired yet. Could be lost cookie by unstable network.
             session_commit();
             session_id($_SESSION['new_session_id']);
             }
            // potential custom logic for session id (ex. switching between hosts)
            $this->setSessionId($this->sidResolver->getSid($this));
            session_start();
            if (isset($_SESSION['destroyed'])) {
               if ($_SESSION['destroyed'] < time()-300) {
                   $this->destroy(['clear_storage' => true]);

               }
            }
            $this->validator->validate($this);

            register_shutdown_function([$this, 'writeClose']);

            $this->_addHost();
            \Magento\Framework\Profiler::stop('session_start');
        }
        $this->storage->init(isset($_SESSION) ? $_SESSION : []);
        return $this;
    }