Drupal Installation running without settings.php (multisite) What we intended to achieve was setup drupal.abcd.com as main installation of multisite setup, and abcd.com, xyz.com, pqrs.com as sub-sites of the multisite setup. 

The main installation (drupal.abcd.com) should contain the default Drupal installation (with the Bartik theme), and abcd.com should have the ABCD theme with content.

drupal.abcd.com is automatically taking the settings.php file from abcd.com. So, when I make change in abcd.com (e.g. setting a different database) the same change is done for drupal.abcd.com.

I also tried deleting drupal.abcd.com/sites/default/settings.php, but I can visit drupal.abcd.com with same settings as abcd.com.

The installation and creation of folders were done by the customer; I don't know what mistake he did. 

Could anyone please suggest me where things might have gone wrong, or what can be done to avoid this behavior, and run everything as normal?
Have a look at sites.php in your sites folder.

 $sites = array(
   'devexample.com' =&gt; 'example.com',
   'localhost.example' =&gt; 'example.com',
 );



  The above array will cause Drupal to look for a directory named 
  "example.com" in the sites directory whenever a request comes from 
  "example.com", "devexample.com", or "localhost/example".


So in your case you should have 'drupal.abcd.com' =&gt; 'default'

The reason why its picking up settings file from abcd.com is because when a request comes for drupal.abcd.com it looks for folder drupal.abcd.com since that folder is not there it will look for next match like abcd.com and it picks it up from there.

I am not sure about Drupal 7 site set up but playing around with sites.php should fix it.