It sounds like it was wrong for other reasons, before UCE came along.  I would not count on IRS "automatically" figuring a refund on an amended return.  I would tell the client not to file the amended return, and offer to redo it for a reasonable fee.  It would help, though to know more details.  Was the amended return to reduce or increase a refund?  How many dollars are involved here anyway?  Is there also a problem with a state return?