Regarding duplicate registration for 12th board exam and its probable effects

Since in your case, you are noticing that there is duplication of the registration number for your forthcoming coming class twelve examination. However, you need not worry for such a duplication of your registration number for the CBSE examination.
Your registration number and Roll Number offered by the CBSE from the next school from where you are appearing for CBSE Board would be valid.
It was the sheer mistake of the previous school to forward your name for registration and on your approach to the school authorities, you have been apprised with the latest developments claiming that your name has been withdrawn from the final list of class twelve students writing for CBSE examination.
Even if you notice a gross mistake where you have been allotted double Roll Numbers due to the ignorance of the Board, it would not impact your candidature for the said board since in the examination hall, an invigilator would approach you for your signature in the attendance sheet. In your case, the Board would find that you have put your signature in a single copy of attendance sheet provided to the invigilator.

Nothing to worry about. You have not done anything wrong. As soon as you come to know that there is a duplicate registration, you have informed the concerned and they told you that they have removed your name and not forwarded it to the board.
The mistake is committed by your previous school. Now they have corrected the same. Now you will be attending the examinations with the roll number given by the present school. There is no chance for the Board to find any mistake from you.
Don't think much about this. Prepare well for your examinations and fare them well.