Can a person from vats gotra do marriage from person of kaundilya gotra?

Yes, a vats can marry Kaundinya gotra. Because they are a totally different vansha tree. Vats originates from Jamadagni and Kaundinya originates from Vasihta so there will not be any health issues and at the same time the yash tatva will not diminish.

You can further consult any param gyani.

Thanks,

Amit