After a silly feeling with drush make and github I found out that all the .git folders (used by git to record history, config, origin location etc ) were removed by drush make and I have heard about this before but didn't come across myself as I was not maintaining the make files.
Specifically drush make removes the .git folder and u can see that if u run it with --debug option
Executing: rm -rf '/tmp/drush_make_tmp_1305733094/__git__/__build__/.git'
In my make file I am fetching 4 things from git repo because I wish to track development on them, 2 of them are my custom components ( 1 custom module and 1 feature which records all the config) and the other drupal core and media module due to high volume of fixes they receive. The whole purpose seems defeated if I can't have respective .git folders but I am also sure there is a way as others are using drush make with git but couldn't find in my quick search.
Thanks for your time!