I'm building a module that has to sync users with another, non-drupal, db. When the hook_user_update is run I check to see if the user has an account in the other db. If they don't then it creates a record there and returns their id from that system. The problem I have is now I need to store that new id in a custom drupal field as well. I don't want to assign it and call user_save inside of hook_user_update because I don't want to run another instance of hook_user_update before the other has finished running. So, is it possible to just save a single user field without having to call user_save thus triggering hook_user_update?
field_attach_update() may do what you need
A comment on the API doc page mentions using it to update a node's fields without updating the node.
If your custom field isn't part of the user object, you may just need to use drupal_write_record to write your field data.