We had a similar but slightly different question, where we have actually had our community running for over a year without taking advantage of the custom domain that comes with our business plan. We are interested in taking advantage now, however, it is important to us to make sure that:
1 - Prior interlinking between different topics in the forum would still work. We have many posts that link to other topics.
2 - The links that we have previously sent over email would still work.
Really scared to make any changes that could potentially break the above. 
Would the redirects be set up by Discourse to make it a smooth transition? Would we need to do anything else in addition to selecting the domain and emailing? Or could there be potential issues?