Let me state the facts for you.
- Yes HEC has dumped the 2 years bachelor program
- Yes, you'll get the degree of your Bsc and everyone else as well who are already enrolled.
- Universities aren't sure yet how to enrol Bsc graduates in 5th semester. This needs to be done yet at University end.
You may apply for Msc after your Bsc. Then you can take admission in MS/M.Phil with other students.
I hope my response was helpful. Feel free to ask if you have more queries.