Bulk Update All Objects
Older versions of Pathauto (4.7 and 5.x-1) regenerate all aliases of the requested type during a bulk update when the Update action (at Administer > Site Configuration > Pathauto > under General Settings) is set "Create a new alias, replacing the old one."
Bulk update replaces all old aliases with new ones. However, this bulk update created problems, such as incomplete updates and/or server time-outs, for very large sites and/or on particularly slow servers.
Bulk Generate For Non-Aliased Objects Only
As of Pathauto 5.x-2.x or Pathauto 6.x-1.1, bulk update only generates aliases for non-aliased objects - if a node already has an alias, it will not be updated during the bulk update. You might run into problems if you add feed aliases or tracker aliases to an already aliased object. It is best to delete the object's alias and bulk update them.
Deleting all aliases
To regenerate all aliases from a clean slate, Pathauto 5.x-2.x and Pathauto 6.x-1.1 provides a "Delete all aliases" option. You can selectively delete by "all aliases", "users", "content", "user blogs", "vocabularies and terms", and "user trackers".
In Pathauto 5.x-2.x the "Delete all aliases" options can be found at: Administer > Site Building > URL Aliases > under the "Delete all aliases" tab (admin/build/path/delete_all).