Reference Based on Two Fields of a Content Type
Is there any reason why you could not just reconfigure auto node title to generate a node title based on a composit account number and environment -- say, something like "[account_number] ([environment])"?  It seems like if you did this, then your reference_account_number configuration would remain unchanged, your feeds will not get confused, and users can still add references by typing the account number only thanks to the standard autocomplete feature of node references.

If you did not like the way that "[account_number] ([environment])" looks in the output of your site, you could alter the render array, maybe in a hook_process_field.  For a good description on hooking the Drupal 7 render process, see The Scary Render Array.