My 3 year old autistic son is suddenly afraid of going upstairs. What do I do to help him overcome this, and how do I find out what caused it?

FEARS. It is common for a young child to have fears and imaginations. Perhaps he has a bad deam that you are not aware of. There's a lot of assurance and care for him to tell you later. Meanwhile, make him comfortable that you are always by his side to help him.
Reassurance . It is not uncommon for a new fear to develop for what seems to be no reason and it is not always possible to find the trigger. If it is associated with increased anxiety in general and/or other symptoms there may be a medical issue. If it is stand alone than behavioral intervention can be very helpful. Enlisting the aid of an applied behavioral therapist is helpful if you are struggling yourself.