I when into the software a day after my return was accepted and added more 1099-R.

[MakeMoreDave]

I received my refund minus the new higher amount, even though the new higher amount was reflected on the turbo tax software after I added the new 1099-R. I was glided on how to add the new software by one of turbo tax agents who called me back. Should I still file a amendment 1040X.

[DMarkM1]

Yes if you updated your interview to add a 1099R after the return was accepted you will need to file an amendment that includes that 1099R.  

1. Sign back in to your account and "Add a state" which will allow you to make changes.  
2. Delete the 1099R that you added after the fact; to get you back to the original return that was filed/accepted
3. Print that now original version so you have a copy to reference for your 1040X
4. Sign out 
5. Sign back in and this time click "Amend" 
6. Follow the prompts to complete the amendment which will include adding the 1099R back in
7. You will be asked what the original return had for certain line numbers
8. Refer to the printed original version you have for those amounts.