Exchange 2007 Creating new mail.que database:
On HUB Servers:
1. Use get-queue command in shell or queue viewer to check that ques are empty.
2. Enter net pause MSExchangeTransport command.
To stop the flow of new messages into the queues on the target Exchange transport server and allow the existing messages to be delivered
4. Use get-queue command in shell or queue viewer to check that ques are empty
5. stop MSExchangeTransport service.
6. rename the queue folder to queue_old
7. start the MSExchangeTransport service
This will Create New queue folder & mail.que database automatically..
Note:– if you are having issues in creating folder then just rename the queue & chkpoint file..
Tech Wizard 
Good One
one note:
If the transport service is paused, then no more incoming messages but the existed ones in the queue will be delivered as usual…if you resume the service again, then the server is allowed to accept new connections (messages)
yes you are correct…