You may not be able to "commit changes" once you try to start using an alternate host that was configured to use another host already.
Your EMWMigration.log file may also hold the following lines or similar denoting the issue when attempting to commit changes on Mail Sync jobs or others.
24/05/2011 19:09:46 MMExCore|Quest.MigrationManager.Exchange.Informer.informer_WriteLogError Error: 0 - (Cannot connect to the Quest Mail Target Agent's database. Path: \\<old-UnwantedServerName>\QMMEXNode$\Mail Target Agent\Config.mdb | Source: aeEMWCommit.JobBase.BeforeUpdate)
The SQL database information may be out of date and not updated properly.
It may be necessary to remove all jobs that are related to the server of the old agent host target. For example, if you were trying to migrate to EXServer1 but are now using an Alternate Host for ExServer1, then removing any pairs configured for sending to ExServer1 would be deleted from the jobs. Changes are then committed.
At that point the ExServer1 can be removed from the database. This can be acheived by right clicking on ExServer1, found under the Target Exchange Organizations in the GUI tree of the project.
Once removed the database is repopulated by renumerating the target Organization server - ExServer1 back. Use Global Catalog to ensure a full repopulation of the database with information.
Recreate all necessary jobs and commit changes.