Recently we had an issue on a transport server where it was loosing connection to network intermittently. There were huge number of emails in queue to be processed but due to connectivity issue, server was not delivering emails. Initially we stopped the MSExchange Transport service to stop this server from accepting any new emails but this resulted in all queued emails which were accepted till that time also stop from being processed.
The solution I implemented was to Pause the MSExchange Transport service.
When MSExchange Transport service is stopped on a Hub server, it will not accept new emails, and will not deliver existing queued emails. By pausing the MSExchange Transport service, it will allow existing emails to be processed but will not accept any new emails.
Later when the network is stable, we can again resume the service for normal operation.