Staging process -- how NOT to overwrite user content/data @ DB push to Production site?
This is a big architectural issue and as answers to the other question says: UUIDs in core in D8 will be a big improvement. They'll give all content a unique ID (independent of the content id in the database), and so if you make important modifications to content in some staging phase, the software could reconcile which content is worth transferring.

There's a UUID project for Drupal 7, which I believe Deploy module can use in this way.


  The integration with Services module alters all UUID enabled entity
  resources (nodes, users, taxonomies etc) to be based on UUIDs instead.
  This way it becomes easier to share and integrate content between
  sites. This functionality is used by Deploy module.