To get around the hub behaviour please increase the hub postroute_reply_timeout.
Please open the hub in raw configure and find the reply_timeout in the <postroute><queuename> section. Please set it to 0 for probeDiscovery, and apply the changes to restart the hub.
The logs will confirm the value is set, for example:
<date><time> [thread] hub: Subscriber 'discovery_server' at '<IP>/51139' attached to queue 'probeDiscovery' (subject:probe_discovery requested bulk:0, granted bulk:1, minimum bulk:0, wait:0, heartbeat: 2, reply timeout: 0), time used: 4 ms
This should allow the discovery server to process the graph and continue to process the rest of the queued messages.