4.5 Beta "msg":"Index Not Found - cause: queryport.indexNotFound","code":12016

No need to stop the server.
You can delete the n1ql cache entry with

delete from system:prepareds where name="…"

(where the dots are the name of the prepared statement).
You also have to restart the application to clear the application cache, or the application will pass again the old plan to the N1QL service.

@krishan.jangid no need to restart the application necessarily, you can call the invalidateQueryCache method on the bucket to get the same effect on the app server (i.e. write a jmx bean to trigger it or some other fashion)