Dear S Namratha,

KEA is yet to release the details of how counselling will proceed for AYUSH 2018 admissions. However if the rules for that counselling remain same as those applicable to Engineering and Medical seat allotment, then If you choose Choice 2 in one discipline (Engineering lets say) and you are allotted a seat in another discipline (Medical for instance), then upon choosing choice 2 in medical, your seat of engineering will automatically stand cancelled and your seat in the latter discipline will remain. 

But remember that you will have to pay the fees if you choose Choice 2. Also, as per the information bulletin of KEA, no surrendering of the seat will be allowed after mop-up round. 

Now, given that AYUSH allotment isn't taking place alongside, it is difficult to say how the dynamics between the shifting of allotment will proceed. 

I would suggest, if you are keen on taking admission on your present seat and do not have any qualms in studying in the said course and college, then you can choose Choice 2, while you will have a window remaining to wait for AYUSH results. 

Just a follow-up question (doesn't impact the answer), were you given the choice of filling preferred colleges for AYUSH courses at the time of choice filling? 

I hope I am able to bring some clarity here. 

Good Luck!