I have a website that has a domain name such like
www.example.com which is of course the website. Then there is
example.com which is used by my boss for remote desktop connection. I was wondering if this will be a problem for SEO?
NO it won't, the RDP uses a specific port that is not part of the usual SEO crawling.
The only issue is if
RDP wont have any effect as its on a different port,