I think it won't create a huge problem. Your name is displayed at least. The portal to change the choice of city, category, gender and paper has been opened by IIT Bombay. There is no mention of changing Name. If you want you can mail the authority directly mentioning your problem. They will definitely help you out.
Check out the link given below and mail your zonal IIT.
https://gate.iitb.ac.in/contact.php
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