I recently submitted my thesis for viva and have since noticed that by transferring from one computer to another endnote has changed my references. The end result of this is that there are 3 extra references at the beginning of the list (which throws out all the other references by 3). Is there anything I can do about this? Are my supervisors allowed to contact the examiners and make them aware? Or do I need to suck it up and face it head on at viva.
Don't worry, it's a very minor issue. In the worst case it will be part of some minor corrections you'll have to do after the viva.
It's important that you don't contact the examiners yourself, as this might be against the rules. Instead talk to your supervisor, they will know what can be done in compliance with the institution rules; and even if they don't they will know who to ask at least.
As far as I know it's usually fine for the supervisor to contact the examiners, but rules may differ by institution, and since the PhD viva is an official examination it's crucial to do things by the book.
Whether anyone will notice/care and what, if any, the consequences are, is completely up to your institution/the examiners.
However, if your supervisors are reasonable people, it's the best to ask them. Maybe they know what can or should be done.