There is a nasty bug in Pathauto module, which causes troubles when you use Views Bulk Operations module (or generally when you save a node programatically).
The problem is that nodes saved via node_save(), do not respect the checkbox "Generate automatic URL alias" on the node. That means, that if you a have node with manually created aliases and re-save them using VBO, for example, all your manual alias are gone as on node save pathauto creates new aliases based on the respective pattern.
One quickfix is to set the system-wide pathauto setting for what to do on updates to "Do nothing. Leave the old alias intact".
As more general solution, there is the pathauto_persist module, which acutually save the pathauto checkbox setting on a per node basis, and makes this information available for node_save. By using this module, VBO can be used to correctly update or not update the path alias depending on the setting for the individual node.
There is also a patch in the work, which aims at merging the pathauto_persist functionality into pathauto module itself: http://drupal.org/node/936222