We have added a couple of mailbox servers in our target domain, they are not showing up in the target migration, so I can't include them in the sync job.
QMM Does not automatically add newly added exchange servers to the organization. In order to use any new exchange servers they must first be added to the project.
To add new exchange servers to your target organization.
1.) Open QMM and select the "Exchange Data" tab in the lower left.
2.) Expand "Target Exchange Organization" out so that the servers are listed under "Exchange Administrive Group".
3.) Right click on one of the servers and select "Refresh".
This should now go through and add any new exchange servers that were added to the Exchange Organization and allow them for use in the project.