Recently I have stumbled upon a situation in Joomla 3.1.1 where I need to add a custom field attached with default registration form.
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Depending on whether you needed the custom field to be added to the database or not, you could use a form building component such as RSForm!Pro or ChronoForms. They both can tie into the user registration system in Joomla and give you a lot of flexibility in custom emails, adding info to database tables, etc. This would insulate you from any core updates that could wipe out your modifications. I believe Chronoforms is free as long as you don't mind a link back to the developers in the form.
If you can't do that, I would make sure that I had a backup of the files that I modified handy before updating the site. Joomla 3.1.x is a short term build so you have a higher risk of those files getting changed than if you were working on a Joomla 2.5.x site.