When you save a job queue or a deployment, it is not saved to the .bps file. It is saved globally (in the registry). The only way, in theory, that you could somehow save the deployments and job queues and then have them seemingly disappear from your saved items, is if you were working with multiple instances of BatchPatch at the same time. If you saved the items in one instance of BatchPatch but then you closed that instance before you closed other open instances, you would lose the saved stuff. This is because the last instance of BatchPatch that is closed is the one that will be saved last, so whatever saved queues and deployments it contains will overwrite anything that was previously saved by another instance.
-Doug