Project 2 Payment will run the sync with QuickBooks for no more than 30 seconds. This is the equivalent to about 200 payments. If the session times out, don't be alarmed. The job didn't fail; it just stopped transmitting.
If you have a large amount of data and everything didn't make it over, simply hit the Sync button to run the job again. Another option is to sync more often so there isn't so much to send.