Normally when a snapshot are deleted the snapshot disks are merged and consolidated to the base disk, In case of the consolidation fails then there wont be any snapshot shown in the snapshot manager.
In vSphere 5.x a new feature has been introduced in the vSphere Client so that Admins can able to check the VM is there is consolidate required without check the VM folders for the delta files
what will happen after I run the consolidate option ? How does this work in the background
Snapshot disk will be merged to the base disk and it work in the same process deleting snapshot from snapshot manager
Will the snapshots come up again in the snapahot manager ?
No Snapshot will not be seen in snapshot manager
Check the below two articles to know more on this
http://blogs.vmware.com/vsphere/2011/08/consolidate-snapshots.html