Yes, we are using IMS Enterprise.
After several meetings and emails with the GenecSys developers and upper management.
GenecSys and Moodle do have different IDs even though they are the same user. It was suggested before (which I do not know of until now) that we have to manually change each IDs of the users to match it from the GenecSys ID in order to prevent duplication. Same with the courses I think.
Since there are developments in our upgrade, the upper management decided to have two Moodle Installations (1 for the incoming semester and 1 to retain for previous students). With this, we will only sync users to the new moodle install with a clean database. The easiest and a wise solution to all other problems with the existing Moodle installation.
Thank you very much.