Drupal Users while developing: Methodology
I would suggest using Features to deploy your changes if you aren't already. That way there shouldn't really ever need to be any database changes going upstream, so this problem will be averted. 

Any database changes that do ned to be made can go into hook_update_N functions in your Feature module's .install file

EDIT

In favour of other popular opinions, there is also the Configuration Management module which attempts to backport the CM functionality from D8 back to D7.


  The configuration management module enables the ability to keep track
  of specific configurations on a Drupal site, provides the ability to
  move these configurations between different environments (local, dev,
  qa, prod), and also move configurations between completely different
  sites (migrate configurations) without the use of modules with all
  configuration being owned by the site.